experience levels for fighters or pilots would be nice. I wonder, though... I guess it would be quite easy to implement experience levels for the aircraft themselves, but if you start to add pilots, you need all those extra things like a pilot assignment screen for the aircraft - that's quite a lot of extra work.
perhaps an easier way, although a little bit weird at first, would be to really let the soldiers be the pilots for xcom's aircraft? you would simply add "piloting" as an additional soldier stat.
for the skyranger/lightning/avenger, the soldier with the highest piloting skill would be taken as "pilot" - that would also explain nicely why we lose the transport craft when the ground team fails.
for the interceptors/firestorm, you would simply set their crew capacity to "1", and you have to assign a soldier if you want to use the aircraft.
if you want to balance this in terms of soldier capacity, you could always increase the skyranger/lightning/avenger crew capacity by 1, and also have the hangar increase your base's living space by 1, too.
it would add an interesting twist: in a ground mission, you have to decide if you want to bring that one extra soldier into the battle or have him stay behind to fly the expensive aircraft out of there in case the mission fails. since the interceptors and firestorm are supposedly VTOL, you might even consider taking on a crashed small scout battlescape mission with the pilot... a high-risk mission, but if your other team is not available, you might try...
