Not a fan of flying mounts myself, but I also think it wouldn't work. The way the game is instanced, some interior areas are put in the 'empty' areas of the map. When you go into Solitude, the map marker shows as you would expect, but the actual Solitude interior is a separate instance way over in central Skyrim (where you can't get... officially). This is also a likely explanation for why Northern and Southern Elsweyr are separated as they are.
Flying mounts would necessitate the reworking of the whole map into a contiguous landmass, with enclosed city areas no longer instanced and actually placed where they are supposed to be. Sounds like a lot of work, and possibly something that with the current game would not improve performance.
This is an educated assumption on my part however, based on things I've seen, encountered or explored, including some OOB discoveries.
Remember when alliance change was never going to happen.