I quite like how Mists of Pandaria handled the whole flying thing. If I recall correctly, you could not fly there until you had basically got to the highest level, meaning that you had to actually explore the land/content before you get the ability to fly.

Given how FFXIV progression is wrapped around the main campaign, it could be feasible that you do not actually get the skill to fly until we beat the expansion story or get to level 60. Anyway, I actually think that flying mounts could increase the exploration nature of the game, what with the floating mountains and areas only assessable to flying.