There's a lot of discussion about flying/not-flying and I'd like to try to sum things up and maybe realign the discussion a bit. Some of the other threads are near-cap, some have really gone down tangents, so I'm just picking this one to throw a reply into. Apologies to the other threads.
We intend to disallow flying while leveling from 90 to 100, and have flying become available again in the first major patch for Warlords of Draenor.
No flying while leveling has been the case during Burning Crusade, Wrath of the Lich King, and Mists of Pandaria. We allowed flying during Cataclysm because as those zones were mixed-in with the 1-60 world it just would have been really jarring to dismount you as you fly into Hyjal, etc. but we would have disallowed it for Catalcysm zones as well if there was a reasonable solution there.
Flying trivializes combat. A lot of people like to say we're trying to force world PvP, or that we just really want people to look at the pretty trees we made, but those really aren't the reasons that drive this same decision we've made every expansion. Flying allows you to escape or enter combat at-will. There's a reason why flying isn't allowed in dungeons and raids, or battlegrounds and arenas, and that's because it would trivialize the core mechanic of the game in those areas - combat. For much the same reason it trivializes how content is approached in the outdoor world based on the simple fact that you can lift off and set down wherever you like.
So that's the main reason. But sure there are a lot of other problems it can cause for content design such as zones having to get a lot bigger because flying mounts can travel so quickly (and thus making ground travel in them take much longer), it reduces the impact of elevation within zones, it completely removes the ability for us to pace or present content in any structured way, and in general removes our ability to determine how and when players approach a situation, see a vista or location, or charge into/out-of a combat situation. It just greatly reduces any gameplay we want to create by allowing infinite choice in how content is approached to best suit a player's intention to (usually) avoid that content.
I totally sympathize with people's desire to do that, they want to be efficient and have it be their choice, but we have to balance our intent to create a game against creating a sandbox where anything goes. There's a happy medium there somewhere, but flying mounts in most cases just do too much to undermine too many of our core intentions with the game world, the basis of the game: combat, or guiding players through a game experience, and for those reasons we have continually chosen (when we could) to disallow flying mounts in the 'current' outdoor content. In the past that's meant only while leveling, but in our experiences with the Isle of Thunder and Timeless Isle we feel like we can extend that for a bit longer in the new content, and have it be kind of a big deal again once you're able to earn flying in the first big content patch, and in the meantime putting focus on flight paths as well as having some more interesting travel options for players to use.