Sorry for the multiple posts, I seem to have trouble uploading large posts. What a shame...

4) [NEW RULE] LOGISTICS (the process, not the technology): It is clear to me, especially from Ugleb's comments, that carriers and starbases with hangar modules will have to be able to spawn their own fighters (ala StarCraft). Just allow them to build short-range ships, one per week, at the same price as a starport.
Limiting them to one/ week may actually be enough to keep carriers from being horribly debalancing... you'll probably lose most of your fighters in a good battle... having to wait for your supercarrier to make 10 new fighters will be a chore. Sure, you could park it over a planet, or transfer fighters from another carrier, but then you have to spend more money and plan.
5) [NEW RULE] To keep things fair, all short-range production (on carriers, starbases, and starports) should have a maximum build time of one week.
6) [CHANGE] No "small"-sized short-range ships. That gets too complicated. Trust me, I've given it a lot of thought.
7) [CLARIFICATION] Carriers can repair their fighters at double the rate ships repair themselves (they are basically a big fighter drydock).
8) [NEW RULE} Another one I thought of before and didn't put in. Hangar modules are just empty space... not very tough. They should probably drop the number of hitpoints in the hull. To borrow from Starfire, I suggest making larger hangar modules that use slightly less space and are cheaper, but take more HP away (because they are larger, continuous empty spaces.
EXAMPLE:
TINY HANGAR MODULE:
10 spaces
carries one "mini" hull
costs X (to be determined)
-0 HP to carrier
SMALL HANGAR MODULE:
19 spaces
carries two "mini" hulls or one "tiny"
costs 1.9X
-1 HP to carrier
MEDIUM HANGAR MODULE:
37 spaces
carries 4 mini or 2 small
costs 3.7X
-3 HP
LARGE HANGAR MODULE:
72 spaces
carries 6 mini or 3 small
costs 7.2X
- 5 HP
"GALACTIC" HANGAR MODULE:
100 spaces
carries 12 mini or 6 small
costs 10X
-12 HP
9) [CLARIFICATION] Hopefully the self-spawning thing will help the AI manage the lgoistics of carriers. However, I agree with Ugleb and Regicide that AI programming will be a problem. I am not sure that any carrier idea will fix this, though. Probably why StarDock doesn't want to bother...

Ok, that's all. I hope.