Firstly I apologies if this has already been mentioned.
I know a few people have suggested rolling contracts for airlines. However an idea i had would be that as part of a contract (rolling or not) once the contract is signed you can assign checking desks to that company so that all flights for that airline can go through one desk.
This is similar to what happens at real airports having check in desks for select companies who have contracts. This will also have the option with new contracts where airlines might provide own check in staff or other options.
Any comments or opinions on this, add away.
PS I have no idea how complicated that could be to bring into the game.