From what I've been reading, there's a lot of back and forth about whether or not flying should be permitted in WoD. Here's what I've gotten from both sides so far:
Saves time and makes the game more enjoyable for those whom have more than one toon to level through the content.
The artwork is nice and all, but it can get repetitive after a while, when you have to go through the same path more and more.
Breaks world pvp to where it's almost non-existant.
Prevents people from viewing the artwork that the dev's worked hard on for the world.
My idea to give everyone a little of what they want, which I'm welcome to creative feedback and will edit my post accordingly to incorporate such feedback is as follows:
1: On RP/PVE realms, incorporate Flying in WoD as a perk for those whom have at least one toon at level 100.
2: Also on RP/PVE realms, once the player has a level 100 toon capable of WoD flying, they can purchase the ability to fly on any other SAME SERVER toon at level 90.
3. On PVP/RPPVP realms in WoD zones, completely disable flying so world pvp is no longer "broken".
4. On PVP/RPPVP realms, while this has nothing to do with flying, an idea to fix the issue of max level players from murdering low level players trying to farm/level grind themselves would be to turn off honor for killing opponents whom are at a lower level than you for those at level cap and those that turn off their exp. Level 100's should need to focus on killing other level 100's, not level 96's whom are still working on those last four levels. (Thank you for the idea Seróquel)
I'm no coder, but from what I've seen them do with things like the Death Knights becoming permitable after one toon reaches 55 for ANY realm, and seeing what they did with the faction rep bonuses in Mists, I believe something like the first two ideas should be simple to do. The third idea would then be a 'realm type check' as soon as they enter a WoD zone and if they fell into the specified server group, they don't fly in those zones until they return to Azeroth.
Edited for idea 4 on 11/13/13