Just an idea that popped into my head, I don't claim it's the best idea, but it could possibly be a middle ground between the "remove flying mounts" and the "keep flying mounts" contingents.
What if you add fatigue to flying? It's hard work...currently our flying mounts can travel the width and breadth of Azeroth without even having to stop for a breather...what if blizz added a fatigue bar with a set amount of time (cumulative) and after the bar runs out there's a 5 or 10 minute cooldown before you could fly again, or you have to feed or water your mount or something like that? For the feeding/watering option, rather than taking up valuable bag space, it could be an ability, similar to the one currently in use for healing your battle pets.
Does this solution make everyone happy? I doubt it, but it seems like a good place to start anyways...feedback?