I realized yesterday, that since we have pilots for crafts now, crafts have technically all stats that soldiers can have. Including PSI strenght and skill, including bravery and morale...
I had few ideas based on that and had to write them down somewhere:
PSI craft weapon
Succesful attack can make UFO land, slow down UFO or disable enemy weapons. Or cancel UFO mission. Or acquire UFO mission info if not in range of H
Pilots panicking
Morale get's down by missing shots (probably some weapons like cannons should have exception), being shot at, being hit, enemy ship size (flat one time check to lower morale with defined ammount). It can cause pilot to disengage and return to base (may be recoverable), pilot ejects (craft lost if last pilot on board, pilot transfers back to base), berserker rage (pilot attacks with everything, maybe even possible ramming UFO?). Miltiple pilots can support each other - panicking pilot gives negative bonuses as long as panicking.
UFO PSI attacks
Don't know how good this could be, byt if X-Com would be able to PSI in crafts, why not aliens. It can disable weapons, it can cause pilot to panic, it can reveal craft's homebase to aliens and start base assault mission.
Pilot suits
Special armors that give pilots better bonuses for dogfighting or even enables their skills to be used while piloting.
It would need a pilot info on interception GUI. Which I think is kinda missing even now. I can mockup something later.