It's obsolete now that we have Legion.
Just introduce a short questline or allow us to buy flying in Draenor and be done with it.
You could have all flying be account wide no need for a cheevo to do that.
A quest on the other hand would be cool - something akin where you learn to tame the primordial winds of Draenor or some generic fantasy thing like that and make that quest account wide like pet battles.
do 1 quest link in a quest chain of flying unlocks for each zone at max level to that particular zone. Account bound.
Like learning to fly in outland against the Twisting Nether, in Northrend against the freezing wind, in Cataclysm against the elemental hazards, in MoP against the mist, in Draenor against the primordial winds and in Legion against the fel-tainted air. The issue would be gone and everything would become streamlined.
To give a taste of my proposition: After you have reached the max level for that particular expansion, a quest opens up in your adventure journal.
"Take to the Skies" - Speak with your riding trainer to obtain a the flying skill
Single player Scenario:
-Chapter 1 the skies of Azeroth - go to your capital city and enlist a flying city guard for the first time: defeat spawned enemies, capture objectives and learn to control your flying mount -
-Chapter 2: Explore the World: you are sent out to different points in Azeroth and need to either deliver something or help with a threat at that flight master point - you get to feed the flying mounts and bond with them like petting them on the head and so on. you get sent out to multiple points.
After you complete this scenario you get a basic flying mount and the flying skill for Azeroth.
Then Dangers of the 'Twisting Nether" opens up:
-Go to Outland and learn to fly in a hostile environment
you get to defeat voidwalkers for void essence. With this void essence you imbue your mount tto be able to resist the pull of the Twisting Nether.
After you imbued enough essence you get sent out to various points - some even on the edge of the Nether to train your mount in flying better: go through loops, resist chaotic visions and defeat foes while there.
After completing this, Outland flying unlocks.
And so on and so forth on Northrend - the icy winds, Cataclysm zones where the elements are harshest: that in particular you need to fight the low high gravitational pull in Deepholm, the scorching desert climate in Uldum, The fiery skies in Mount Hyjal, Survive underwater in Vashj'ir, and the Twilights hammer in Twilight Highlands. After that the mists in Pandaria etc.
Once a quest link from this chain is completed a by a character, it unlocks flying for all other characters on the account for all zones of that expansion.
This system is much more in tune with the unlocks, and offers a fun alternative to grinding