1)
Was thinking something along the lines of giving the planes and vehicles pilots and drivers. They would then be able to level up just like the soldiers. Like the pilots could learn to dodge lasers better or become better at shooting down certain types of space ships. Vehicle crews could get more action points when they become better trained or improved accuracy and so on.
There could even be some sort of survival chance for the pilot, where he could eject and then travel back to X.N. base.
Vehicle crews could climb out of destroyed units and then if they survived the mission return to fight another day. After a trip to the sick bay of course.
2)
As to the destroyed equipment, I was thinking that the destroyed hunter husk could be repaired at the base for a fraction of the cost of buying a new one. Thus giving the engineers something to do. Could also incorporate some sort of engineers improving hunter armour or sights or rifles to improve the gear. To give them something to do while research is under way. These improved rifles could be silencer, larger clips or larger calibre bullets for the assault rifles.
Comments and other ideas welcome. Thanks for taking the time to remake a classic and keeping the feel of it.