I really like the idea of having aircraft that have to be carried on a starship like a tank would be. I also like the idea of construction units being used to make aircraft more efficient at their roles by building airbases and what have you.
Aircraft should also be significantly reduced in efficiency if the atmosphere is thinner or thicker than normal racial average, and utterly useless in non-atmospheric environs. There could be specialized aircraft made for light or heavy atmosphere (separate research to expand this!), but they have reduced efficiency outside their normal scope just the same.
So far as aircraft role, I'd argue that these should be customizable. You have 1.0 to apply to all the different potential mission parameters. So, for example, an air superiority fighter might be 0.8 air superiority, 0.1 CAP, 0.1 strike, and 0.0 SEAD. There could also be a stealth aircraft research that when applied multiplies the cost of the fighter by 3x (or more), and de-prioritizes that unit in targeting.