I still want to hear the response to this!
You have put a lot of thought into your doctrine, but how well would it hold up with the upcoming introduction - on both the UEF and GTVA sides - of capship-fired countermeasures?
That would entirely depend on what countermeasures we're talking about. I need specifics; how expensive are those countermeasures, what is their nature, how widely are they available on their fleet's ships, how effective are they, etc?
Regardless, I can't think of any countermeasures that would reduce the Ballista's cost effectiveness from "crazy OP" to "not all that cost effective". Remember, they can jump to anywhere in Sol in a few minutes, without warning, and jump back in seconds, provided the time was taken to charge up both drives beforehand.
So, say, those refineries, fuel storage/cargo, and stations in the second to last mission (where you "bait" the Carthage)? Here's how you do major damage, both on a strategic AND logistical level, without any losses:
1) A group of 20-30 Ballistas charge up both their drives. A third are just equipped with anti-fighter/turret missiles, a third have half of that and half bombs, and a third have just bombs. An Aurora fighter, or maybe even a Pegasus for maximum tactical advantage, "maps" out the area ahead of time, and if needed, helps with the jump calculations.
2) The Ballistas jump in. Any fighters or turrets in the area have no fewer than three Trebuchets (or a dozen Harpoons, or three dozen Tornadoes) fired at them within ten seconds. Provided that there's no immediate threat, the two-thirds of the force equipped with bombs goes after their designated targets--fuel and supply "crates"/storage, refineries, tankers, etc; potentially even the stations themselves. Any surviving fighters are finished off with further salvos of anti-fighter missiles; on the very off chance that a few survive anyway, the time they spend trying to evade and just survive is enough for the rest of the Ballistas to complete their objectives.
3) After hitting their targets, they jump right back out. Enemy jump-5 response teams arrive minutes afterward, finding absolutely no enemies to attack, pursue, or track.
So, there you go. You can pull off operations like that frequently, inflicting major damage to enemy logistics/supplies, morale, and the enemy's strategic initiative. Any potential countermeasure or countertactic would have to adequately protect all such potential targets. That also means that, even if they work, the Ballistas have already pulled their weight because they're tying down a ton of enemy resources, personnel, craft, and even potentially ships.
But it's important to remember that any effective countermeasure to the Ballista would have to also be, by nature, an effective countermeasure against shock-jump tactics and/or massed missile salvos--even for individual fighters. Such countermeasures would be massive game changers to combat and strategy as a whole, not just to the Ballista.
There is, MAYBE, one already existing counter to Ballista strikes against capships and fighter wings--AWACS. Except that this is apparently false, as every mission in which you have an AWACS on your side--FS2 or BP--enemy missiles still lock on to you and track you just fine. Jumping in and out works just fine as well. So that doesn't really work, then. Even if it did, AWACS ships are rare and valuable strategic assets, and are thus not going to be seen outside of battlegroups or fighter wings on critical missions.
Missiles 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.
Ship AAA either can't shoot down a given type of missile because of a flag setting, or they can, in which case the usually slow missile/torpedo is shot down with ease unless fired in large numbers or up close.
Torpedos are absurdly slow; a WW2-era torpedo travels faster, and its booster/engine is a tiny propeller--and the torpedo has to travel through water, which tends to be rather thicker and more friction-y than empty space.
The end result is that missiles and torpedos do not behave anything like they should or like you'd expect, and the "balance" is screwed up. And the warheads are nowhere near heavy enough to make a rocket engine so ineffective/inefficient at propelling the damn things. When gravity completely and utterly outmatches rocket boosters of over three hundred years in the future in terms of giving torpedoes velocity, you have failed so hard I can't even begin to describe it.
Not that you need to upset the gameplay style/dynamics of Freespace to fix it. Just make all missiles "shoot-down-able", but have longer ranges across the board and/or faster velocities. To make things easier and more fun, have the HUD automatically passively highlight/target missiles in your area (or heading towards your area), to make evading and destroying them easier and more fun.
In terms of anti-ship torpedoes, here's what you'd do:
1) They have longer ranges (how much is up for debate/testing)
2) They have MUCH, MUCH faster velocities. This is to make them harder to intercept, practical beyond point blank range, and far more dramatic on both sides.
3) They would do MUCH more damage to capships, depending on the type of torpedo and type of target. So, say, some torpedoes are designed to be effective against destroyer armor, but do less health damage, while other are only effective against lighter armor but do much more health damage (so it would do negligible damage against a destroyer, because of its much heavier armor).
4) They would, depending on the type, take up a lot of space. Only bombers, or craft similar to them, would be able to carry them at all. Depending on the yield and rating against armor, they'd either be things you could only carry two of on medium/heavy bombers, or two of on a light bomber (that's just the gist; the idea is that mnongo torpedoes for use against superdestroyers would be one or two apiece on heavy bombers, while a light bomber could carry one or two less powerful torpedoes for use against cruisers, etc.)
Alternatively, they'd be dumbfired in order to render ECM and countermeasures useless, but would have very fast velocities; this makes lining up a shot something that requires skill unless you're close up, and it also requires efforts to prevent it from getting shot down by either fighters or AAA. Keep in mind, though, that was much faster velocities, it won't be the "snails of doom" that torpedoes currently are.
Anti-ship torpedoes would be completely distinct from anti-subsystem/turret missiles; they'd behave more like heavy anti-fighter missiles that have intelligent enough tracking to hit the target even if it moves a little).
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As for how Ballistas are able to jump in accurately enough to be in good positions from the moment they exit subspace--the answer is twofold.
1) For cases in which you need to be precise in a narrow window of opportunity, you need an AWACS or sufficient sensor/whatever support via several Auroras or capships. Thus, this would only happen in cases where the target(s) is high value and/or critical, or when deploying an AWACS (or enough equivalent assets) is not risky or costly.
2) For cases in which you don't need as much precision, or you have a larger window of opportunity, you'd either have indirect support (like from command, more distant AWACS, or previous, uncoordinated scouting) or you'd have one or two Auroras (or Pegasi, scouts, etc.) in the area to provide assistance and report the effect on target (if the Ballistas can't stick around to find out). Given that an Aurora is common and not exactly expensive (BP lore is a little unclear on that), this makes strikes/operations like this easy and relatively cheap to perform.
With fighter or ship cover, Ballistas can also operate without jumping out right away (or after striking the targets), as in most cases they'd outrange--or outgun at range, with FAR more missiles. Even with just a 40MPH/KPH (which does the game use?) engine and no afterburner, it would still keep up with (and in some cases outrun) any ship (SHIP, not fighter/craft).