Yes, but not the way you are thinking. Flying mounts with wings and all, but don't make them fly way above ground. For balancing issues, I would say just make them hover closely to the ground. This
Flying mounts are one of the worse things that can happen to games like this. People just stand in town waiting for a queue to pop. If you have a quest mount up fly there and disregard all the stuff
Although, as a few have posted interest in dragon mounts, dragons have no mention of being around at the point in time ESO is taking place. Alduin won't show up to resurrect them for a very long time.