Couple of proposals
Slot restrictions, Airports have times when flights cant take off
Gate restrictions, currently airlines can have hundreds of gates at an airport, even though in real life there would not be the capacity that is in the game.
Ability to build own terminals
Ability to open multiple official bases.
Ability to sell and lease back aircraft.
Hedge Fuel
Issue bonds (Instead of taking out loans)
Ability Negotiate gate and landing fees