As I said, they already gave you all the reasoning behind their issues with Flying.
Whether they add it later or not has a similar thought process to the changes in their decisions regarding Garrisons.
A lot of people criticize Blizzard for announcing they want you to pick which zone your Garrison is in and then going back on their word.
Those people either refuse to see or are simply oblivious to the way things are designed in a game with such a huge scale.
Everything you add, remove or change in an MMO as big as WoW creates ripples, and Blizzard needs to account for all those consequences - often fail to handle all of them, but at least try.
So let's go here through a small thought process - something I guess they do all day everyday:
What if you could pick where your Garrison is?
The Garrison is connected the advancement of each Zone, so in order to have your Garrison in a Zone that is meant for a higher level, wouldn't that mean you need to skip content to get your "favorite Garrison spot"?
What if you could pick where your Garrison is WITHIN a zone?
There would be phasing issues. If there are 6 spots to place your Garrison within an area, that means for any player there will be 5 empty spots.
So how would that be handled?
First, there would be no quests there.
Second, would there be anything there? Wasted space or equal mobs/nodes/etc?
Would there be a garrison that you can enter but really belongs to no one and has nothing?
Possibly the best solution, what if you have an Outpost in each Zone, but only one of them becomes a full fledged Garrison, and you can choose which one that is (the others remain mere Outposts)?
Even here there are some issues.
This either inhibits Blizzard from or greatly multiplies the development needed to add any sort of events linked to the advancing and/or upgrading of Garrisons.
So although Garrisons may seem a non-issue that Blizzard is making a big deal out of, if you think a little you'll find many holes in ANY solution you try to present that attempts to make us able to choose where our Garrison actually goes in Draenor.
The same goes for Flying.
It's not "fine", and there isn't a super easy way to fix it.
I've made a topic about it in the official forums -
The Future of Mounts (Constructive) - but it's not a perfect solution either.
So armchair developers need to keep their egos in check and respect the those actually working in the development of a successful game.