Well, i have an idea, like Tenacitys, but without the ability of commanding the fighters.
Can't you create a weapon (like a torpedo or rocket launcher) which launches AI-fighters instead of missiles/torpedos. The fighters will belong to the players faction, for example a Guardian for Libery-Captains or a Templar for Bretonians. In case of equipping it would be the samce as Tenacity proposed: armor upgrade and class 9 faction guns.
Of course, this weapon and it's "ammo" (the fighters) must be very expensive, but the one who can afford a carrier or a battleship, is also able to buy this, i think.
The weapon/launcher would only be mountable on battleships / carriers and i think it gives the ship-owner the feeling to be the captain of a "real battleship" or a "real carrier". Also, this would make a battleship or a carrier more worth as support units in battle events, where the captains of those ships can support the other players by launching those npc fighters.
Maybe, you can edit it that way, that if the carrier/battleship gets destroyed, the fighters which are launched also are death, like in starcraft with the protoss carrier.
Thats my idea of a carrier / battleship;)