From what I've played, my aircraft was almost every time losing against UFOs, so having a pilot seems useles unless the aircraft doesn't get destroyed everytime. I'm imaging that the pilot gets xp and performs better as times passes by.
If you are going to implement a pilot, then the pilot should be (in my imagination) like a soldier, able to use weapons and equipment, but once he's dead, you can't take off, so it's your gamble if he fights or not. The pilot should have some mediocre combat stats, though, or basic training like close weapons, etc.
However, X-Com and other similar games didn't feature a pilot, and I didn't feel that he was missing. In Fallout Tactics any squad member could drive the car/tank (some were better drivers than others). OFC piloting an aircraft is different, but I was thinking that a pilot isn't essential.
