Input on Carrier Caps:
All Caps: I was just doing homework and had my calculator handy, and wondered what would be a good SC cap - 10 sounds like a nice, round number, but you don't get them all until level 10. Starting out with 2 SC, that's .8 SC per level (rounded down). So, it works out such that at level:
- 2.8 (2) SC
- 3.6 (3) SC
- 4.4 (4) SC
- 5.2 (5) SC
- 6.0 (6) SC
- 6.8 (6) SC
- 7.6 (7) SC
- 8.4 (8) SC
- 9.2 (9) SC
- 10.0 (10) SC
That makes them carry a crapload of fighters w/out becoming too powerful straight away.
Sova:
1. Embargo - The suggestion for making Embargo act like a PJI for other ships is a nice idea - it could be explained away by saying that the Sova actually HAS a portable PJI on board the Carrier that's been tweaked to specifically target trade/refinery ships, though it still affects the bigger fish.
2. Missile Batteries - Instead of lowering the AM cost, why not make it deploy additional Missile Batteries at each level? 1/2/3, 1/2/4, or 1/3/5 all sound like good ideas, though 1/3/5 might be a little too powerful.
3. Heavy Strikecraft - I'm not sure what all the fuss is about this ability, but then I haven't really paid attention to all the chat over it, so a lil' summary may be needed... 
4. Rapid Manufacturing - Maybe to make this a bit more desirable, all carriers w/in a certain range, including the sova (say 5-6000 km) get the instant SC. And why not make the 30% a full 100%? Or 50-75% if that's a bit too extreme.
Skirantra:
1. Repair Cloud - Probably its only redeeming factor. And it's a "fire and forget" ability, unlike the Progenitor's Shield Restore, which REQUIRES it to remain motionless. I don't see much that needs to be improved here.
2. Scramble bombers - as most others have said, this needs to be GONE. I never, EVER saw a need to get this. Instead, perhaps something to the effect of Charged Missiles for SC could be implemented? Though that would make the Junsurak a moot point...hmm...
*snaps fingers* I've got it!
Nanite Shockwave: The Skirantra releases a massive discharge of Nanites from its hull, disabling enemy abilities and also collectively linking their fates, causing them to take an equivalent amount of damage spread across the affected ships. Costs 100 AM.
LEVEL:
- Range - 4000 km, 15% Damage is shared
- Range - 6000 km, 30% Damage is shared
- Range - 8000 km, 50% Damage is shared
These are, of course, subject to opinion, but I thought I'd throw it out there.
3. Microphasing Aura - Seems fine. Leave it.
4. Replicate Forces - Also fine.
Halcyon:
In all honesty, excluding Anima Tempest (maybe Adept Drone Anima, as well), this ship is fine. Though, as stated, the name "Anima Tempest" would imply that the fighters usually "pew-pew"-type attacks suddenly become a STORM of laser fire that rips the enemy to shreds. All it does is create 30 additional fighters, which, when you think about it, is somewhat like Scramble Bombers on steroids.
Instead, why not make Anima Tempest make itself and all friendly Carriers in a, oh, about 5000 km radius suddenly give their fighters a MASSIVE DPS boost - on the order of 200-300%, even, for about 60 seconds. Certainly gives the name a whole new shine. 
Anyway, my 3 and 7/8ths cents.