any idea that fixes the problems with fighters being weird needs to let fighters operate in fleets and on the battlefield without a carrier on the field, this is what the devs really wanted to maintain.
Here you can read the reasoning for the current fighter system and the thought that went into it. It seems like the reasoning for the odd and somewhat wonky way fighters work right now is to give carriers something to do, as, if fighters didn't need carriers on the field there would be no reason for them at all, but they want to maintain the whole "able to deploy without a carrier" thing.
Then theres the thing about multiple flight decks, it really is somewhat pointless to have more than 1 flight deck on the field right now, so if we could knock that out too that would be optimal.
I'd reduce hangar capacity on most things that aren't carriers, maybe even reduce some of the carriers. the amount of extra hangars even the most fighter heavy fleet ends up with is way over the top, so it does sort of invalidate the idea of dedicated carriers to a degree. Next i'd say that carriers cant regenerate lost ships even with extra supplies, and say that landing a fighter on a carrier frees up fleet points, allowing you to deploy another fighter as soon as you land one for re-arming/repairing. i'd also make the time it takes to redeploy fighters much longer
You'd still be able to deploy fighters from off screen if you didn't have a ship with a flight deck (or if you didnt deploy your fight deck ship), this makes the flight deck benefit a place to rearm and repair to a degree but a place to launch fighters in the middle of combat, first of all. The flgiht deck would probably also have to be given a much longer re-arm time to justify having multiple flight decks
Another possibility (could be an alternative or both used together) that would really amplify the power of having more than 1 flight deck is the possibility that each fighter wing would get a spare number of fighters based on how many flight decks were on the field. lets say, you have a single odyssey. Each one of your wasp wings would be able to return and relaunch up to 6 individual fighters, while multiple flight decks would be able to launch up to 12, or even 18. If this is implemented i would make it so that if the wing is destroyed it doesn't actually count as destroyed until you launch all the spares, as one of the wonky things is that the whole fighter wing would be lost forever if you didn't get half a drone back. the justification could just be that the fleet point cost has a lot to do with interlinking of ship communications, systems, and data or something, which would explain why you cant just have all the wings that are in storage with spare pilots on the field. its just the FP system in a way.
One other thing is that i dont think crew losses are taken into account mid-battle for fighters. If fighters are being sent out then flying back and rebuilding themselves, it should be noted that each time it does that you'd be losing lots of crew. right now it just seems like it calculates it based on the health of the wing at the end of the battle, which of course doesnt make sense because you can just repair before the battle ends and not lose any crew.