I think the only way where we have control over a pilot in ground combat should be when something has gone terribly wrong. Downed dropship/transport maybe, and we need to evacuate the pilot along with the survivors. Or a Search and Rescue mission for a fighter pilot after ejection. These are, however, very specific "negative" scenarios and not very applicable to the gameplay, I fear.
On the topic of stats and perks for the interceptor pilots: hell yeah, I'm all in! I don't know if perks should include special maneuvers, though, or it would end up like something along the lines of those Sid Meier's Ace Patrol games
What I do want, though, is painted UFO kill marks on the nose of each pilot's fighter craft. That would be so cool.