One thing I've noticed while playing AE is that when scheduling flights, you can only make direct flights between cities, and you aren't allowed to make a route Via another city.
For a simulation trying to be extremely realistic, this doesn't make sense at all as airlines make passengers go through other cities to connect to flights all the time.
It would be a very simple mechanic. While you are setting up routes, there would be a button to either:
1. Add a city in between the destination. (ABC---*GHI*---DEF)
2. Extend some flights from the destination city. (ABC-DEF-----*GHI*)
3. Offer connecting services (Basically if you are outside your home country you could operate 1 route out of that city as if it was your home country, but it must use the same plane and correspond with the original flight's schedules, and you can't offer any other flights outside of that airport unless they are to your home country or as another connecting flight from the original) (ABC-DEF-DEF-JKL)
If you were to set up a multi-stop flight, you would select a certain number of flights or create some flights, and it would be like setting up a route normally (Check if the plane could make it, the demand for that stopover, etc.)
It would appear like:
508376: ABC-DEF Via GHI
It would take more working hours, and services on the route would cost more.
You can only set up about 3-5 Stops between destinations.
Let me know your opinions or suggestions below!