Quickly reversing after announcing that flight would essentially be a thing of the past in the run-up to 6.2, Blizzard instead implemented a set of achievements that would unlock flight account-wide in Draenor. The method here was, I think, rather fair. Essentially, you had to really experience the on-the-ground content, getting the loremaster achievement in each leveling zone, doing the various level-cap daily assaults, and doing a significant amount of Tanaan Jungle - enough to get revered with the three factions there (something that could be accomplished after about two or three weeks of dailies,) and finding several Draenor Treasures (something that is pretty easy given the availability of treasure maps for all those zones.)
On one hand, I understand the rationale for keeping flight restricted. Keeping you on the ground means that to scale a mountain, you have to fight your way up a path - they can design that path to be an adequate challenge, and make reaching the top feel like a real accomplishment. They can make a heavily-guarded fortress feel like something you really have to fight your way through to kill the general in the center. And flight can trivialize some of this questing content.
In the past, we've seen expansions where you unlock flight at the level cap - this was true in Burning Crusade and Mists of Pandaria. In Cataclysm, flight was unlocked immediately, and in Wrath, flight was unlocked at level 77 - right before going into Icecrown and Storm Peaks, two questing zones that absolutely required the ability to fly.
It might not be surprising that I prefer the Wrath model, but the BC/Mists version also works out pretty well.
Even with daily quests, Blizzard has never really made outdoor content the main event at the level cap, so in a real sense, hitting the cap is a pretty strong "you've completed this content, so feel free to fly over it" kind of milestone.
I think you could potentially justify the restrictions on flight during Mists of Pandaria, when there was a ton of content (even if it was a pretty unpopular set of daily quests in 5.0) out in the world you'd be expected to complete after hitting 90. But that argument actually falls apart a little in Warlords, where there really wasn't much to do "outdoors" at 100, at least until Tanaan Jungle. The main outdoor content was in specific assault areas that you could have easily made into no-fly zones while making the rest of the zones flyable.
Ironically, by making the flight achievement account-wide, you actually introduce the worst-case scenario of flight, which is a whole leveling experience that involves dipping down and striking at enemies with impunity.
Though how "worst-case" is this? I've finished leveling my Druid and Priest post-flight, and I've got to say that it was a pleasure to be able to fly around while doing it. Then again, I already know these zones like the back of my hand, so it's not exactly the typical questing experience for most players.
Storm Peaks and Icecrown show that you can make wonderfully compelling questing content that include flight (I used to just hang out on the Skybreaker or Orgrim's Hammer because it felt so cool to be hovering above Icecrown on an airship like that.) So I actually reject the notion that flight ruins questing.
But I do appreciate that some zones benefit from that limitation. Restricting flight allows you to force players to explore for paths and also lets you hide things in clever ways.
Ultimately, though, once players are at a point where that exploration is no longer compelling gameplay, it doesn't really make sense to keep flight restricted.
Going forward in Legion, I'm going to keep an eye on what world content exists. If there's tons of questing left in the Broken Isles (before they add new zones, which could easily be made flight-less like Isle of Thunder or Timeless Isle) then I can understand the delay on unlocking flight. But if it's like Warlords, where there's really not much to do outside... well first that would be bad in general, but it would also make the restrictions on flight just kind of spiteful at that point.
Flight is a part of World of Warcraft, and while on any project, you've got to be willing to slaughter some sacred cows, I think that the lack of flight in most of Warlords was not the right call. Had there been a Draenor Pathfinder achievement in 6.0, or even 6.1 (making that patch good for something, at least,) it would not have been as much of an issue, but Warlords has gone quite quickly into the "winding down" phase, and so the fact that flight was unlocked two months after the last major patch (probably shouldn't have said "weeks not months" about that,) it comes a bit later than I would have hoped.
I hope that we see a revitalized outdoor game at level 110, and I hope that part of that game involves flying (preferably between airships and floating islands in the sky, because dammit, this is fantasy!)