I have some ideas I want to suggest, but as I only played a bit of the mod some of these might not work as well as they do in my head.
1. A hullmod that increases the fighter wing size (and replacement rate to compensate) at the cost of firepower/damage done, basically the idea is to trade crew casualties to spread out the damage, so losing one fighter would mean losing a smaller amount of firepower. Or alternatively, this is probably harder to make, but have extra weaponless decoys added to the wing to soak up damage.
2. A cheap/free hullmod that reduces fighter cost (well, cheap enough to not make it cost more in total), but the fighters will be severely weakened, the idea is to mount sub par versions of high cost fighters on weaker carriers.
3. probably some endurance core for the carriers that give them better replacement rate recovery at the cost of the carrier stats, like slowed speed or cut down flux to use for the replacement recovery.