WoW has designed such zones.Now, imagine zones that are made to be traversed in the air. Then you don't have that immersion problem anymore. Just look at Vashir. That zone is effectively a flying zone, since flying and swimming in WoW are the same things, mechanically. It is possible to design such zones.
Vashj'ir is pretty hated tho, despite my personal love of it, which is why I think Nazjatar was not made a water zone.
Storm Peaks was a levelling zone designed with mandatory flying (you could rent a flying mount if you did not have one) and people found it frustrating to navigate through. I remember in Cata people saying Vashj'ir was Storm Peaks but worse. Icecrown was also mandatory flying (since the quest hubs were air ships) but it's a lot flatter than Storm Peaks was so it wasn't as bad to navigate.
Wrath was a rough patch for flying with their experiments at zones designed with flying. the PvP zone that was a no-fly zone in the middle of the continent didn't help.
But that was years ago and Blizz does have better mechanics and more experience so personally I would like to see Blizz try another crack at a zone designed for flying.