I'm almost certain that this has been talked about before... but.
To take away flying would ruin the game at this point. So the only option left is for Blizzard to embrace flying and make zones, islands, questing areas etc; only available through it. This was done in Wrath I believe and I remember it being a really enjoyable experience having to fly to the top of Storm Peaks or wherever it was; as it was the only way to get there.
Embrace this mechanic and make it a true character of the game's design. Don't just have it as an ease of access tool to get around the zones. Having that as Flying's only benefit is ~ B O R I N G ~.
It's a subjective topic I suppose but, am I wrong?