I'd definitely like to see more dynamic air combat, with more realistic weapon loadouts, more interceptor and fighter types and more weapon variety. I'd also like to see one where damage to enemies carries over from one interception to the next... as well as to the tactical map.
Maybe an option to target specific areas of an alien ship, or random hit location allocation. Then check to see what alien crew are in that section and apply damage to them (to kill them or have them start wounded). Different weapons might have different penetration and/or effects. Same procedure for components. Thus destroying the engineering section in air combat would likely end the combat quickly, causing the ship to lose power and engines and crash...killing the engineers onboard, but also destroying power systems and engines, so no chance of recovering those or fuel sources in the missions. Targeting the enemy crafts weapons would mean they can't shoot back, making it safer to attack, but stands little chance of downing the enemy craft and means you can't recover alien craft weapons. etc. etc.
Base this on the damage done to the ship, maybe by section/compartment. Damaged, breached, destroyed values maybe.
Then of course, this damage would be reflected in the ship model for tactical combat, both exterior and interior and create more dynamic entry points.
Maybe options to bomb or strafe the site and continue the attack as the craft goes down, or has already crashed...which would cause more damage and kill more enemies, making more breaching points, more options and an easier mission...at the cost of more aircraft ammo, less experience for troops on ground, and less equipment and components that can be recovered in tact (less alloys from the hull too, obviously).
Give more strategic and tactical options and flexibility, at the cost of more choices...balance your needs.