I personally like the idea of no flying until 6.1, mostly impartial though.
However, I think an extremely negative effect will be on faction dominated PvP servers. All of my 90's are Horde on Bleeding Hollow, an extremely horde dominated PvP server.
The Alliance players are going to have a terrible, frustrating time leveling through WoD that makes me even pity them. Not to mention I'm sure it's going to be frustrating enough for a lot of them to server transfer, making the imbalance even worse.
Realistically though what can be done?