I like the idea of a drop tank that can take the place of a weapon. Or perhaps aircraft can have mod points (in addition to hard points), for other such add-ons. Your chinnook could also have these (drop tanks would be invaluable).
Drop tanks for longer range.
ECM/ECCM/Radiation scanners for searching for UFO's/Bases/Activity.
Defensive systems (flares, chaff, alien-tech) for defeating missiles or enemy weaponry.
Afterburners for faster aircraft.
Deployment packages specifically for transports, such as flare-droppers in night missions, or field scanners that give a 1-turn indicator of likely locations of aliens, etc.
Etc.
Drop tanks would be invaluable early game, when you can't afford global coverage. Likewise, on a chinook you might have to balance between a drop tank (to get your best guys to further destinations) or a defensive package (so they get there safely).