I've thought this for a while but having leveled up through Pandaria it really hit home with me. There were a few times where I was frustrated and wished I could just fly to an area, but it got me thinking that I would never get that feeling if flying was never in the game in the first place. The game is just so much more engaging if you're looking at it from the ground. When leveling to 90 I had to look where I was going, think about my route to a questing area, figure out the best order to do the quests, etc. Once I hit 90, I just picked up a quest, mounted up, point myself in the right direction, and hit num lock. When you're on a regular mount you notice and appreciate the surroundings. When you're flying, you just notice the yellow arrow telling you where to go.
I always played on a pvp server in vanilla. I never even though twice about it. Why would you want to go kill dragons and get a big axe if not to smash some other players with it? But when TBC was released I didn't start right away mostly because my raiding guild had broken up when they added paladin gear to the raids(funny how something so seemingly small could break up a guild). So I was a few months late, enough time for most players to hit 70 and get their mounts. When I started questing is was horrid. I was getting ganked left and right. No one really corpse camped me but it didn't matter because I had no way of escaping - I was helpless. The best part of pvp was random encounters out in the world but that was completely taken away with that one change. Leveling became extremely frustrating and I ended up transferring to a pve server to play with a coworker. Now I'm not some cry baby that whined every time I was killed in pvp. Far from it. I went through the gauntlet of STV and BRM in vanilla and loved it. But the addition of flying mounts just made it.....different....not fun at all.
I think flying mounts are cool and some zones are designed great for them but I just have this overwhelming feeling that adding them was the worst single thing that ever happened to the game. There are plenty of other gripes I have about the game - arenas, the hard separation of pve and pvp(it blows my mind that pvpers complain about being 'forced' to do pve content), cross realm stuff, etc but I thought this was the biggest. I think a huge chunk of the nostalgia people have for vanilla could have been sustained for much longer if flying mounts were never added. When was the last time you were blown away by something in the game that wasn't forced upon you(with some sort of cinematic)? I'm thinking of stuff like entering blackrock mountain for the first time, going to ungoro crater and seeing your first devilsaur, etc. I had countless experiences like that while on a ground mount and maybe one or two on a flying mount.