How about being able to edit map hex properties so that the hex would be impassable to units with flying or floating (or some other type of movement ability, due to high winds or something)? Of course, there would have to be a limit on how many types you could ban, eg flying, floating and mountaineering all allow for crossing mountains, so any combination of two of these?
This would make it possible to deny strategically important map objectives to those who get flyers early and prevent using a single dragon to take such a location if you don't want to put excessive defenses there. Another way to do this would be to give structures a property that prevents flying units from joining combat as long as the place is controlled by independents (perhaps by setting a flag value that is nullified the first time somebody captures it).
Of course I realize that this might be a headache to implement,but it's a thought. Whether or not it gets done, I guess we'll see when the game comes out.