First, you could create the FAA to regulate the number of takeoffs and landings at airports. I don't have specifics, but I imagine that even JFK couldn't dream of handling the number of flights in and out that AE places on it. So in a way that Houston's Hobby Airport has a governmental restriction on the number of passengers to out of state airports, airports could be limited in the number of takeoffs and landings. Right now I can fly as many flights out of Jackson, Mississippi as I could out of Chicago, granted the passengers wouldn't be there. Limits such as the one above would impact the bigger cities tremendously. Just because you have a passenger demand and Bombardier fleet for hundreds of flights between Chicago and JFK you should be limited to something reasonable since other airlines need to use the airport also. So a total available slots for takeoff and landing commiserate with the number of gates or terminals you operate.
Second, more focus on the airline's formation in the beginning could drastically change the game. Along with your initial terminal and aircraft force players to select either the spoke and hub or point to point business model which will come with pros and cons for each. Spoke and hub would have a reduced maintenance and personnel costs since it focuses on operating out of one or more hubs potentially. Cons to spoke and hub could be an increased ground time since it would have more aircraft operating out of key hubs. Point to point would be the opposite of spoke and hub with other potential perks to offset the cons (maybe a small percentage of pax boost similar to an alliance bonus for more direct flight).
Lastly, by allowing airlines to "contract" with certain aircraft manufactures, airlines receive a discount for purchasing from that manufacturer. I know historically that railroads purchased the majority of their locomotives from the same manufacturer and only occasionally ventured from their comfort zone for motive power. I am assuming airlines do something similar. That's the carrot. The stick is purchasing from another manufacturer other than your contracted manufacturer should cost you out the nose (something like a 25% hike of the base price). And if purchase costs for non-contract manufacturers goes up, then so too the maintenance costs go up.
No one of these alone will likely serve as a remedy. All together may still only make a dent. Having actual AI airlines in place may drive down passenger prices. Further, more emphasis on ratings would be a deterrent. Force airlines to spend more to get the lion's share. If you have people packed on a plane where it is standing room only, then passengers should only pay pennies while if you have a plush airline they should pay with Benjamins. Just some thoughts that others can add to or point out why they would fail.