I've already modded my fighters nerfing them. Assault fighters are now tiny hulls instead of medium and only come with missile tech. The interceptor fighters only use beams, and the guardians only use kinetics. So they no longer bring every weapon type to the fight.
I'm also thinking I will greatly increase the maint cost of the carrier modules.
Carriers should probably be one of your most effective ships, but currently they kind of trivialize combat. Packing a ton of little fighters around and or fabricating them "between battles" should probably be much more expensive than the module currently costs.
What we need to do for silliness, is force those fighters to spawn with their own carrier modules! Battle starts, computer explodes from billions of fighters appearing.