Slammers has been said. Darts aren't bad.
For primaries, the Cavalier is a beast of a weapon (and energy based). Maybe UX Accelerators (ammo is a big concern). Warship weapons, the Khatvanga (Point Defense Turret).
The Rapier and Cavalier are 2nd-generation Prometheus derivatives, I guess the Alliance may understand how they might benefit from those weapons (comparing what techniques the Feds used to make them, compared to the GTW-5 Prometheus S).
We haven't seen UX Accelerators in action (but I'm guessing they're not going to consider it because the Maxim already suits anti-hull needs, unless they consider how most of the UEF ballistics have a hell of an anti-shield punch, don't take my word for it)... and god forbid I keep insisting (despite not in any official missions), the Sidhe. Come on. It murders bombers frighteningly efficiently.
Yes, the Sidhe is an excellent weapon in many regards. It's fantastic for dogfighting and almost ideal for interceptors--since they can close the distance better than any others, they can get within effective range of a lumbering wing of Shivan bombers and kill all four of them in a matter of seconds with primaries alone. It would make the Draco actually practical (beyond the stupid ROF penalty for using linked primary banks being removed in the ai-profile table), as that extra chunk of speed would actually translate to better interception performance. The Sidhe also does considerable hull damage against smaller warships, as well.
As for the Maul, Rapier, Scalpel, and Cavalier:
Maul--yes, if practical. It's more energy efficient than the Prom S, does more damage, and is less technologically sophisticated in some ways (no advanced fire control system).
Rapier--depends on how much it costs, compared to the Prom S or Kayser. It's not nearly as demanding in terms of energy, and it's more flexible/versatile than the Kayser for sure. It doesn't have that great of damage, but it's basically a 4-damage increase over the Balor per shot, at the same rate of fire (though not cycled, which is good, as it makes it a better dogfight-oriented weapon from the Balor) with greater range and velocity, at the cost of modestly higher energy consumption.
Scalpel--Not sure, but probably yes if practical cost-wise. It's got the advantage of being an effective shield breaker as well. However, the energy consumption on that thing is monstrous.
Cavalier--if not too expensive, then god yes. It's got very reasonable energy consumption, great range, acceptable rate of fire, and unparalleled hitting power on a per-shot basis (for a conventional energy weapon). I once tried equipping Cavaliers onto both banks of a Perseus, and it wrecks Shivan craft (save perhaps the Dragon, who is still ludicrously hard to hit with anything).
Now, the UX Accelerator: I know ammo is an obvious logistical concern, but what about restricting it to elite squadron and SOC use? It's performance is exceptional--it takes less than one of its 4-shot bursts to kill even heavy fighters or bombers, has a very fast velocity and excellent range, great hull and shield damage (can't remember about subsys damage), and tolerable energy consumption. It doesn't need to be mounted in large numbers to be devastatingly powerful--one or two is still very effective.
As for the missiles in general--several of the UEF missiles are basically more refined versions of GTVA ones, with a few exceptions. The Harpoon is probably better suited for use against Shivans, where the extra punch is more useful than the slightly faster lock-time. The Trebuchet and the Grimler is sort of a toss-up: extra damage might make the Grimler more useful for taking out the tough Shivan heavy bomers and heavy fighters more efficiently, and the range reduction isn't as crucial these days due to a more modern (with a better general speed) fighter force. Importantly, the Grimler has a faster refire delay, which means you can lock-and-fire several targets in a row without any delays beyond the aspect lock, whereas the Trebuchet has a refire delay that lasts a few seconds past the aspect lock time.
The Dirk is probably a good choice as a replacement for the Hornet, as it is a better weapon for attacking bombers than the Hornet (which is largely garbage against fighters in all but the best hands); the big range boost helps a lot. It also provides a decent anti-turret weapon that can significantly outrange the SAAA.
The Shrike versus the EMP Adv...seriously, there isn't even a contest. At all. The EMP Adv was completely impractical from the beginning (sort of like the Infyrno in that you have a very narrow margin of error between successfully deploying it within range of the enemy AND yourself). It is very short ranged, slow, and is almost guaranteed to get yourself caught in the blast.
Dart is a good missile overall, but nowhere near the Tornado. After the Trebuchet, the Tornado is undoubtedly the GTVA's best missile. To be honest, if it was cheaper to just produce more of the Tornado than replace Hornets with Dirks, it'd make the Dirk just plain obsolete.
Hellfire versus Tempest--actually, I don't really know about this one. I'll have to go and look at the stats again. The Tempest always feels more effective, but it seems like it shouldn't be.
Currently blobs and AAA are the only decent bomb interceptors on GTVA ships, so getting rid of them would be a bad idea until pulse turrets can be made more accurate, no?
For the AAA, yeah. But the blobs? I'm skeptical. Pulse turrets are actually pretty decent against warheads; though somewhat inaccurate, they have good range, good rate of fire, much better velocity, and each shot does substantial damage. So even if TT2's are a bit better at warhead intercept, STerPulse's can do (roughly) almost as well on top of good point defense against fighters/bombers and a light secondary anti-ship armament.
If you want a dedicated, effective warhead interceptor, why not just use a Maxim? Not only does it have much better range and velocity (and vastly better ROF), it doubles as a light anti-ship weapon and modest anti-turret/subsystem one, too. As far as energy requirements go, even if you have to lower the ROF to be roughly equal, it's still worth it easily.