These are ideas I have based on real world experience that could make things more involved.
1) just like adding more FA's to an aircraft's configuration helps we should be able to hire additional ground, logistics, and customer service personel to increase passanger ratings. One of the largest differences between a legacy airline and an ultra low cost carrier is personel for the job.
2) Weather tie ins. I'm not computer ace so I can't really tell you how to do it but on the FAA and other websites you can find airport delays etc due to weather. It'd be cool to add a little artificial intelligence to the game where your flights can be diverted, canceled (no financial hit since it's an act of God just no income), and ground delays. To combat this you'd hire extra crew schedulers and flight dispatchers to help increase the efficiency of the operation. If you skimp on either your aircraft will take longer to get where they need to go possibly causing canceled flights later on. With more schedulers and dispatchers you could bring those probabilities down kind of like maintenance percentages.
3) New form of alliances. I think if you are in an alliance you should automatically have IL agreements with every member. Have a fee for being part of the alliance. The director can then use these funds to do things like pay for IL agreements, marketing/advertising, and pay the salaries of personel working the alliance. It would be interesting to give the alliance the ability to help establish slot swaps, routes, etc.
4) IL agreements with improved cost for creating or disabling. Right now it's a click of a button but there should be money tied to is so people are more picky when chosing someone. If someone quickly accepts then backs out they should be penalized.
5) Negotiable fees and supplies. If an airline is going to make a hub in St. Louis then they should pay less in landing and other fees then someone doing one flight per day. Also players in a declared hub should be able to negotiate fuel contracts. This could be a plus or minus for the player depending on how much fuel they buy and when they buy it. It would not be a requirement but a separate market to purchase large contracted quantaties of fuel could add a whole new dynamic of the game.
6) Airlines that declare a city a hub should receive a form of marketing boost or additional pax/cargo demand.
7) Slot swapping. There should be the ability to sell or swap slots to other players. These swaps would be subject to approval just like Department of Transportation does now.
8) Airline marketing. Airlines could put up to X% of funds per week for to increase their pax demand. Take a look at airline-empires.com to get a quick look at what they did. Basically you spend a percentage of income and it increases your ORS rating.
9) Ability to sublease aircraft or form fixed fee contracts. Just like United, Delta, American etc in the United States it'd be fun to buy regional aircraft and then contract that flying to maybe new or smaller players.
These are just random thoughts from my idle mind. I'm sure if you change one variable you change everything so I'm just tossing it all out there. Have a good day :)