People have probably come up with these ideas before, but i couldn't find them in the suggestions or in the upcoming updates section (called something like that). I would like to see:
Premium Economy available as an option, possibly with the option to make it either just an economy section just with more legroom (suitable for regional flights) to almost J class level service with comfortable seats.
Cargo. One thing that did and has annoyed me is that there is no cargo in airline empires, when in real life, a good chunk of many airlines profitability comes from cargo, even belly cargo. This might be a difficult feature to implement, but it could work. Possibly, a distribution centre (built at an airport at similar costs to a terminal) would be required by an airline to operate aircraft that can carry more than say 5 tonnes of freight.
Ability to lease spare gates at a terminal you own to fellow alliance members. This is a realistic feature, a reasonable number of airlines do this in real life (al la Iberia operating to T5 at Heathrow). The gates could even be leased at a much lower cost than the usual airport gates (like a good alliance-mate) and could benefit from an increased number of connecting passengers (due to it being easier for passengers to connect between flights)
The ability to offer limited time sales on routes. This would have the advantage of boosting route reputation and load factors, but would obviously reduce profits
Ability to choose to charge for certain parts of the IFE. In real life, quite a few (full service) airlines offer free AVOD IFE, but charge for Wifi and Cellphone use in flight. I would like to see this offered in AE.
These next two features have definitely been mentioned before, but i think they are a priority:
Stopovers. This feature is an absolute necessity in politically restricted worlds, as at the moment, it is ridiculous to even contemplate ultra long haul routes (such as SE Asia to East US and South America), which in real life exist, because not even the 777-200LR has the range to operate these routes. Stopovers could easily be implemented: you cannot base any aircraft at the stopover city, any aircraft operating stopovers must operate to the stopover city from your home country. To prevent abuse, there could be slot restrictions on the number of stopover flights you can fly. Also, the aircraft could have a maximum occupancy of 50% full fare passengers plus 50% "connecting" passengers, to simulate the passengers that would leave at a stopover and the number that would get on, and this 50/50 would be reduced if the route faced competition. Also, this would mean that that any airline that operates from the stopover city as a home city could still compete effectively, because it could get a 100% full fare load factor.
Seat Types. The ability to choose to have either lie flat, angle lie flat or recliner seats in F and J to either maximise comfort and rating or save space and increase profits, or apply to regional routes. Also, airlines could choose from bog standard, rock hard and cheap seats in Y or leather, comfortable seats that increase maintenance costs but result in greater passenger satisfaction.
Dream Feature:
Tweakable maintenance costs which lead to:
Crashes! Hear me out on this one, I understand this will likely annoy a lot of people if it is implemented, but I believe this feature would be awesome. It could combine how much you pay your flight crew as well as how much you spend on maintenance to calculate the odd of a crash. For example, to save money, you reduce spending to your maintenance department and cut flight crews pay. This saves you a lot of money, but increases your chance of a crash. meanwhile, if you go the other way, there is very little chance of a crash. This would actually introduce consequences for airlines who pay their employees peanuts, because at the moment theres only a reputation drop, which an airline can easily operate with. However, a crash could be such a significant financial drain (compensation, etc) that the airline might either go under or have to buck up their ideas
Well thats my list off the top of my head, there will probably be some awesome ideas i come up with in about 5 minutes but thats it for now