I’d like to see fighters deployed as a module on a cruiser size ship. You could still design your fighters as before, but have them installed as a module on a cruiser. They could modify the pilot count of the cruiser as needed (so 1 module on a cruiser would be 17 pilots I think).
In addition you could have fighters set to return to the cruiser at a certain level of hp to repair, possibly using the cruisers repair modules to modify repair speed.
I think this would help the overall balance as well as provide the carrier capability that makes more sense than fighters just flying around on their own.
Cruiser goes down, fighters lose their repair functionality.