In my opinion, the biggest issue with flying is that once you get it, it just feels like a massive upgrade over ground mounts and taxis. Provided you're not one of those people who love exploring every nook and cranny, you will always pick flying over other options. I mean, why wouldn't you? It's the fastest and most convenient way of travelling that makes all the alternatives look pale in comparison. So... you fly. It's fun at first, but you kinda hate yourself for skipping a lot of content and as it usually happens with things you do all the time, it gets really boring and frustrating in time. Then you either end up finding a way to make your character fly while you go AFK, or you try to use something else, but while it's fun for a while, you quickly realize that flying is way better and since you've already experienced most of the content anyway, you go back to flying.
And thus, at some point flying becomes mandatory for almost everyone and other travel methods such as ground mounts and taxis are completely useless. But... What if Blizzard balanced them out? I'm talking about something like:
1. Flying - convenience at the cost of speed - your movement speed bonus is the lowest out of the three options, but instead you can avoid all the ground obstacles and trash mobs in order to get from point A to any point B completely uninterrupted
2. Ground Mounts - moderate speed and convenience - while you can't avoid mobs and terrain obstacles, you gain a higher movement speed bonus that allows you to reach more accessible locations fastet than via flying
3. Taxi - speed at the cost of convenience - your movement speed is the highest out of the three options and you can avoid everything that's on the ground, but you can use it only to travel to a selected set of locations
Wouldn't something like this make people alternate between various travel methods? Like - there's a horde of mobs or some other terrain obstacle between you and your objective? No problem, you mount up and take to the air - while you don't move as fast, you still get there faster than via ground mount. But if there's, say, a really nice road between where you're at and where you want to go, you saddle up and ride there because it's faster than flying. Oh, and if you want to go to a different zone or travel longer distances? No problem, you just pick taxi and go make yourself a coffee or whatever.
I believe that having reasons to use all three travel methods would make the game more fun and varied - sure, it wouldn't be as convenient as having OP flying mount, but at least it wouldn't be that boring. And the best thing is - the player would get to decide how he wishes to interact with the content. Personally, I think that would be the best way of tackling the "flying issues" a lot of the people have, because right now... Hell, it doesn't really matter how long they delay the introduction of flying - sooner or later it will come back, because people got spoiled by how convenient it is and once the content starts to get old, masses will demand it and Blizz will give it to them. And once it does come back, most people will skip a lot of content and a lot of issues we might have with flying will return. Nothing gets fixed by delaying flying - the end result is the same, the only question is - how much time it will take before we reach it.