WARNING: MEGA POST AND HOURS OF THOUGHT AND WRITING BLOWMissiles in FS2/BP don't really work as you'd expect them to, or realistically, both in terms of using and countering them. You can't shoot them down (well, all but a few kinds of missiles anyway), and they're easy to evade unless in large numbers or when evasion is more difficult. They also have absurdly short range--a modern medium-long range anti-fighter missile has a range of over ONE HUNDRED KILOMETERS, and travels at speeds around Mach 5. They're maneuverable and not at all cruise missiles, either. The decades-old Phoenix missile the F-14 Tomcat used had a range of 190KM and traveled at Mach 5, and a Tomcat could carry at least four of them at a time.
Careful - this way lies madness. 
I'm not trying to apply total realism here; I'm just using it to make a point. Which is below.
I think you've made a good case for your dedicated pop-up Treb strike platform, though I think you're slightly overselling its capabilities against maneuvering opponents; a good human pilot will simply never be hit by Treb fire, and the AI suffers only because it's just not very smart about fast aspect-seekers.
Erm, the Ballista is far, far more than just a pop up Treb strike platform. Remember, you can jump in to within 2000m of a bunch of fighter wings, and fire massive salvos of missiles of any kind--Slammer, EMP, Harpoon, Tornado, Grimmler--you name it. Sure, human-players can dodge a couple Trebuchets, but how effectively can they evade 20 Tornadoes, two Harpoons, and a Slammer all at once? If it's hard for an experienced, good player, then all but the best pilots in the setting would be dead meat in the face of such an attack.
Against capships, again, you could jump to 2000 or 3000m, and launch a hailstorm of Grimmlers. Even if they could be shot down like Stilhettos, some would inevitably get through. Congrats, you've just taken out a frigate's engines and half of its AA capability (or its torpedo launchers, maybe?). You're free to send in a cruiser or corvette with some fighter cover to finish off the stranded frigate. Or, if they bring reinforcements to protect it while trying to repair the engines, so do you. Why not have a destroyer jump in to kill it and its backup (if the UEF brings one of its irreplaceable destroyers, then it's game-on; you can take out any AWACS ship they might have with another Ballista strike! Hooray! Or counter it with your own AWACS, if need be).
Capships launching flares will degrade some of the salvo into missing entirely, and decoy other weapons so that they strike the hull instead of their targeted subsystem.
Flares? What? None of these missiles are heat-seeking! They're all radar, ladar, laser, or dumbfired! Chaff would never work, even on a larger scale (you can't make it look anything like the ship or a subsystem, and without high speed maneuvering, the entire dynamic/system/nature of chaff is rendered moot; you'd also need a gigantic amount of chaff for even a single usage, which is just plain impractical or unfeasible on capships)! You'd need ECM, and good ones. The only kind of ship that demonstrates that in any combat capacity is an AWACS ship, and those are rare and fragile.
And there's no way the UEF (or even the GTVA) could develop and implement such a system so quickly. I mean, we're talking years, unless it's your top priority, to deploy an effective version of it on more than a handful of ships. Rushing it would make the whole thing vastly more expensive, too.
To give you an idea, it'd be like implementing today's stealth technology onto naval ships. We've done it, yeah, but it's extremely expensive and took years to develop, and it's so cost-prohibitive that even the freaking US Navy--weilder of 11 supercarriers and 10 medium carriers, along with many advanced and large nuclear subs--is very unlikely to make more than a few, at least for a long time.
That's for passive ECM. Active ECM is more like those "R2-D2" missile intercept systems that USN carriers have, in terms of cost and scale; they're expensive, took a while to develop, and even today are too expensive to mount on non-capital ships. Israel's Iron Dome took years to develop, costs quite a lot per unit, and is still only a few in number despite it being a very high priority for Israel; they're building several more, but I hope you get the idea.
It's much easier to implement on fighters, because it's on a different scale and level: they're like flares, in that they allow you to use advanced maneuvering and high speed to dodge the missile; FS2 capships are snails. Unless you can quickly move out of the way, the countermeasures won't work; they work by essentially putting a fake "you" where you were a second (or half second) before, while you sharply maneuver out of its path.
Otherwise, you'd need to take them Up To Eleven (
https://www.youtube.com/watch?v=aOx_wHhitqk); the scale you'd need for capships would make this unfeasible. Flares are much easier to launch, are far more cost/space efficient, and are ACTIVE countermeasures, as opposed to chaff, which is more passive--it's just metal. You can design a flare that, despite being the size of a mouse, burns like a super-hot fireball--even though it only lasts a few seconds at best, that's all it needs. Chaff is basically scrap metal. It isn't launched so much as released, and the high speed and maneuvering of the jet distances the chaff from the jet. Capships have no such option. You'd need a massive amount of chaff, launched at high speed, for it to work at all. Additionally, the chaff (and the pattern it makes when launched) would have to somehow look like missile's target. Which is a massive, slow warship. Have fun with trying to make
that work.
But creating interesting doctrine for Blue Planet isn't about figuring out an optimum tactic that can 'win' the setting; it's about creating an interesting doctrine with strengths and weaknesses that lead to exciting gameplay and interesting stories. Even Steele, beloved as he is, is written with some key flaws. So here's my challenge: can you go a step further and come up with disadvantages, difficulties, and countermeasures applicable to your doctrine? Troubles that might be encountered in implementing it, and tactics that might be adopted by the OPFOR in response to it?
I think they're one and the same, actually. You make an acceptably fair playing field (or as fair as you want the story/setup to be on a grand level), set up consistent rules, and try to come up with the best tech and strategy. The limiting factors are meta; what's a faction's economy and infrastructure like? Its culture? Experience? Etc.
In this case, let's say you implement the Ballista for the GTVA, and it works as intended. What's separating it from being immersion/story-breakingly OP and an exciting, fun, and realistic (in-universe) development?
There are three main factors in play here:
1) The UEF's capability. Sol is supposed to have an industrial and infrastructure capacity that rivals the entire GTVA (or at least its Terran side). Granted, that was BEFORE the GTVA invasion, but still. Where are the UEF's production capabilities? It doesn't seem to actually have any--Uriel fighters are apparently an endangered species. New warships are unheard of. War materiel is vastly more valuable than people. Why is this the case?
This big, secret project Bei is working on would explain it, true. Though how such a project would stay a secret really stretches suspension of disbelief, as most the UEF's industrial capacity is being directed to a single, massive project, even as a desperate war of self-defense against a vastly more powerful enemy gradually gains more and more ground. The fact that the project's very existence is almost treated like a rumor by Admiral Calder himself--when speaking to the other two top admirals of the UEF--makes no sense. You'd expect knowledge of the existence of some secret, big UEF project to at least be widely known, especially for morale purposes.
So, this is really the biggest problem: the UEF is just too weak, and far too incapable of replacing losses (aside from poorly trained pilots or cheap fighters), along with showing very little capability to develop new technologies/designs. It can adapt its tactics to a decent degree, but it has yet to adapt technologically, logistically, or militarily. These are legitimate and logical disadvantages of the UEF, which are made even more apparent against the incredible adaptability that the GTVA has always displayed (though its lack of a new fighter capable of reverse thrust and afterburners is puzzling). Thus, in designing some kind of counter, it's got to be mostly tactical in nature.
2) Lore and gameplay contradiction. The UEF's big advantage is supposed to be major fighter superiority (which is itself partially due to the UEF's military being strictly designed around the expectation that all conflict would only be in Sol). In game, this isn't the case, as only the best UEF fighters are superior to GTVA ones, and only the Uriel is a major threat to capships (unless you have space dominance, which means you're going to need enough fighters to match the GTVA in such a battle), and considering how the UEF can't replace its losses, and the extreme adaptability of the GTVA, this should no longer be the case at all. The UEF is running very low on good pilots, has few Uriels left, has lost about a third of its fleets, has taken increasingly serious infrastructure and industrial capacity damage, and has poor morale. After the events of Delenda Est, it seems like the only thing stopping the GTVA from literally just committing to a large fleet action and decisively winning the war is the time it will take to repair and resupply its forces in Sol.
Actually, wait. The Vasudans are likely giving military support now, and they already started giving major logistical support earlier, too. So yeah, I give it a few months at best before the GTVA launches a final assault and crushes the remainder of the UEF. If they decided not to care about taking a bit heavier losses, they could launch that assault in under a month.
3) The UEF's diminishing capability, along with extremely bad morale (that's only getting worse). There are also the internal divisions, to make things even worse. The UEF has two hopes (three, if you count conditional surrender):
A) The Fedayeen. They'd need to be very powerful to make the difference, though. Notably, they'd need to be the War Gods times five, tactically/strategically and militarily, to delay the now-inevitable all out GTVA assault. Stopping it is out of the question. If the GTVA manages to launch their assault even remotely on time, then the Fedayeen need a major, potent technological trump card to prevent the UEF's ultimate defeat that day.
B) AWACS...sort of. The GTVA would need to not develop any countertactics or counter-technologies, and the remaining UEF AWACS ships need to be protected at all costs. And the UEF would have to have at least a few of them to actually make much of a difference. And they'd have to survive and remain operational throughout the battle, which means that no fighters or ships can get shots off at them--a very difficult challenge, for a UEF fighter force that's got few experienced/good pilots left (most of its ranks are poorly trained rookies, flying craft that merely equal typical GTVA fighters)...unless all of that info was only with regards to the Third Fleet, and not the First or Second, which seems unlikely. As it is, frequent raids on various parts of UEF assets/territory during the few months before the final assault are going to make matters even worse, and every good UEF pilot or fighter killed is an irreplaceable loss. This kind of environment is exactly where the Ballista would excel: experienced/good pilots and craft are stretched thin and relatively few in number, the UEF is struggling to protect its various assets around Sol, and the UEF as a whole is fatigued and running on very poor morale. The Ballista can essentially strike anywhere in the entire UEF territory (conveniently limited to just Sol) within a few minutes' time, and quickly jump away. The end result: AWACS is not going to cut it, especially if the GTVA's own AWACS can counter it.
***
So, in the end, what is the UEF's limited counter? A new missile specifically designed to counter massive missile barrages, deployed tactically, like so:
1) It'd be similar in concept to a Slammer--a missile that becomes a cluster munition when the time is right. However, it's area of effect is much larger, and its payload isn't explosives.
2) The payload is something like ECM. Since a vast majority of Freespace missiles are not heat-seeking, flares are not going to help much at all, and chaff isn't going to work either (the missile couldn't carry enough to make it effective over an area), so you'd need something somewhat new. It's supposed to screw with the missiles' targeting/tracking/maneuvering (pick one or two; all three would be ridiculous and hard to explain lore-wise), not destroy the missiles. As such, this missile would need to "hit" the barrage of missiles, which means being in a position to intercept that barrage fast enough. If you're the target, all the better (have fun with that one
). Lore-wise, it could be something like radiation, or even just an EMP.
EDIT: Just found it.
http://www.hard-light.net/wiki/index.php/GTM_EMP_Adv. ||| Yup. There you go. The counter. In fact, this is exactly the kind of ECM you're looking for. Forget flares. Launch an EMP missile at the incoming torpedoes/missiles from a battery in the ship. Obviously, you'd risk affecting your own systems/ordinance/fighters if they're in the EMP radius, so ideally you'd have a smaller EMP missile; the smaller AoE is still sufficient against missile barrages that are tightly packed, but without as much collateral risk. They'd also be cheaper (hopefully), smaller, and thus capable of being more widely deployed, and usable by more craft.
If you're worried about EMP spam, then you can play around with it in a number of ways. Maybe this new class of EMP missile has a "weaker" effect, resulting in less annoyance for fighters, but still sufficient to temporarily disrupt missiles (the canon lore says that the "current" generation of EMP missile affects deeper levels of circuitry for longer effect). Maybe they're still expensive enough to limit usage/deployment (as in, only one of the fighters in a wing has one/two, or each of the fighters can only carry one, and they're only used against mass missile barrages/large Treb strikes). Maybe the core materials comprising the EMP missile are not ones that the big secret project needs, so this is the one new tech/weapon that sees significant usage in the UEF? Maybe standard fighter shielding against EMP has improved since the Capellan Era (possibly even as a mere side effect of improved, standard armor technologies), so fighters are less affected while missiles aren't?
***
As for the tactical adaptations/counters--well, as a preface, it's ironic as hell that what was originally a major advantage for the UEF (the war and their territory all being in one, very developed and populated system) is now a major weakness. The Ballista's strategic effectiveness is greatly diminished in an inter-system conflict; they're dependent on a carrier/ship capable of carrying them in order to use jump nodes, and jump nodes themselves are huge bottlenecks that can also be extensively monitored from a distance; if an enemy carrier/destroyer enters the system, you will know it right away. That also means that a Ballista's origin, home, and base of operations is directly known to you. The first counter is the most simple: attack and destroy their home ships. Ballistas are far more effective--and safe--on offense than they are on defense. If you attack their home on your own terms, you're directly removing the Ballista's advantages, and you can effectively deploy your own specific countertactics and countermeasures without spreading out your resources/defense far too thinly; you have them exactly where you need them and where they'd be effective, and nowhere else. Their only advantage would be their large missile banks, and likely large numbers, but with EMP missiles (which you'd need relatively few of), you're fine.
But that's not at all an option for the UEF, even if we weren't in this unique theater of war. A direct assault on GTVA destroyers--even just one--is a massive and risky operation that requires careful planning and good execution. And a lack of Xanatos Gambits from the other side. And you have to actually destroy it, not just heavily damage it. Worse yet, the GTVA has a number of destroyers in Sol already, in addition to several available bases of operations (such as the captured Artemis station).
So how does the UEF counter it?
1) Centralize and consolidate your forces and assets. This makes you more vulnerable to a large, direct assault by the GTVA's Sol fleet, but hopefully they won't be capable/willing to attempt it for at least a few months while they repair and resupply. Despite their victory in Delenda Est, it came at the cost of heavy damage to a lot of ships--the Carthage's entire battle group is severely damaged, with only the Carthage in good fighting shape. The UEF assaults that coincided with the operation must have also inflicted significant damage or casualties, too.
This will make it possible to adequately defend a vast majority of your forces and assets, and avoids attrition warfare, which is very bad for the UEF in nearly all cases, at this point. This will leave quite a bit of territory vulnerable, but it's a necessary sacrifice to buy time. In order to counter another Steele Gambit (TM), you'd have your forces structurally divided into several cohesive, powerful battle-groups. Those battle-groups would only respond to major, credible attacks, while the rest would remain consolidated and "close" to each other, deterring against a major assault against your core fleet/infrastructure/assets. GTVA has more destroyers in Sol than the UEF does--counting the Meridian, it's something like five or six to the UEF's three. The UEF, having just lost four frigates and two cruisers in Delenda Est (in addition to any losses from the other engagements that day), can't afford to send anything more than a single cruiser and transport to any non-major engagement. Thus, small, coherent strike teams of fighters are also organized, designed to respond to minor raids. If a GTVA cruiser shows up and you lack Uriels or bombers, too bad; retreat.
If more than one GTVA destroyer battle-group attacks a significant asset/thing, then you will not counter it with a second Solaris battle-group. You will give it up. This is because it's a clear and classic Xanatos Gambit--they win whichever way you act--but choosing to engage would result in disaster, rather than ceding that asset/territory. Instead of losing a refinery or city, you'd lose a Solaris, or the most critical/core of your infrastructure/assets. Either one would mean that ultimate defeat could be expected as early as a week or two afterward.
This strategy is all about buying time. You're giving up bits and pieces rapidly in order to conserve your core and most vital of assets, as well as your ships, which are the only thing standing between the GTVA and total victory. Samuel Bei says he and his project just needs more time. Well, here's his time. It's as much as he can get, short of a ceasefire to sue for peace.
Ballistas are going to incur heavy losses either way, but this strategy will limit those losses to less important assets and territory. Otherwise, they'd allow the GTVA to bleed the UEF ship by ship, squadron by squadron, major asset by major asset. With a consolidated force, infrastructure, and assets, you won't be spread thin, and even the best Ballista strikes would not be able to chink the figurative armor.
2) Focus defense on military and essential assets, at the cost of leaving civilian and nonessential assets with token defenses. The hope is that the GTVA will be far more hesitant to destroy purely civilian assets, ships, and installations. If they do anyway, then it's a boost to UEF morale, moral high ground, propaganda, and hurts GTVA morale, support for the war and the GTVA. It also helps in negotiations--not just moral high ground, but also less willingness to refuse to budge on terms on the GTVA's part. There's definite guilt there.
Ballistas can't really capture that stuff. Their hit and run attacks with mass missile barrages kill and destroy and leave as short a presence of force as possible, by design. Thus, if the GTVA instead tries to capture those assets/ships/territory, they'll have to do it without Ballistas, and they'll have to post forces there permanently to keep it under their control (even without threat of UEF attack; they're UEF citizens), which means less GTVA forces capable of attacking you.
Ships on the level of corvette and above are to be preserved at all costs; each such loss significantly hurts their chances of being a match for the GTVA's Sol fleet should they decide to launch a direct assault. Thus, committing them to action must be done carefully and conservatively. If need be, cede the asset and save your ships. It might be getting to dangerous levels of fuel in sixth months, but at this point the entire UEF wouldn't last
three if you start losing ships.
A great many mods have put time and effort into coming up with awesome new ships and awesome new tactics, but Blue Planet always strives to create things that are interesting but in some way flawed.
Honestly, you've got an intertwining of story, setting, and gameplay here. You can have weaknesses reflected in other ways than gameplay. The M1-Abrams tank is a good example; it's got speed, firepower, heavy armor, ruggedness, range, etc. But it's more expensive for it, not just in terms of building one, but in maintenance costs--a jet engine requires a lot of maintenance after rugged operations in a desert. Using that incredible speed means using a lot of fuel, so you need a good supply chain. And, you know, fuel costs money.
Thus, the UEF could come out with a new Solaris--one even equipped with AAAf beam cannons. Or it come out with a new fighter--one like an Uriel, that is effective against fighters yet also a major threat to capital ships, and even equip them with EMP missiles as standard issue, and build a ton of them relatively quickly, with production picking up steam instead of waning. The cost? Tons of money, including diverting resources away from things like schools or the economy, as well as shifts in public opinion (positive and/or negative; the morale boost alone might be more than worth the financial cost). If you go far enough, you might even start to compromise the ideals that Ubuntu stands for (economically speaking). But you'd survive.
Thus, an "OP" in-game element becomes balanced in the overall blend of story, setting, and gameplay. You could also have the other side, UEF or GTVA, come up with new tactical and technological counters, to keep the in-game balance where you want it. Maybe a specific new fighter is quite OP, but is so expensive or difficult to produce that there are very few of them. Maybe this new torpedo [Helios] is a huge step up in terms of power, to the point where it's a significant threat to even the Atreus [SJ Sathanas], but is so difficult to produce and prohibitively expensive that they're only deployed in the most vital of strategic circumstances [Capella] by the most elite pilots [Alpha 1].
See what I mean? And regardless, you can always just alter the competitive in-game balance too.
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