As far as I know, the planes do have a single seat for trooper right? why not just use that slot somehow and have some affect on the air fights?
I mean pilots can have: maneuver, close and long range fight skills, and experience (which comes along, not start from 0. Could be "mind" perhaps?)
I would think pilots with more experience plays better than some noobs who are trigger happy and not able to judge the situation from previous engagements. Well, close enough since I don't think any of them have ever fight a UFO before their first flight...
And as other troops, the pilot can hold equipments and weapons and armors to increase survival rate. I mean plane got shot down doesn't always means pilot dies with it. Could be that they ejected and/or down with the aliens and have to fight for survival.
Then maybe the plane can be equipped with even more things like , escape pods, parachutes, etc, for higher pilot survivability rate if the plane got shot down. Can still add those now for the survivability of the troops if the landing ufos ever got up and attack the transport..
Edit: it seems i spoke too soon without reading it all. i guess it was already suggested.