What stuff are you skipping in MoP by flying? What legitimate, engaging content was made in any expac with flying for that matter that players just hovered over it thinking "That looks cool, all that down there, I'm just gonna sit up here though".
In places where Blizz wants us to be on the ground to engage it on the ground, they do so ala IoT, IoG, the Thrall Torment chain, Argent Tourny, TI, MF, IoQD etc. They haven't, however, restricted our freedom on how we get there before.
We fly to the places we want to do content, we get on the ground and do that content, then we fly to the next lot of content we want to do. All with the choice to stop and admire that view, kill that rare, harvest that shiny, explore that hidden cave, help that guy leveling kill that mob, do a 180 and mail that thing I just remembered, or fly full bore to my intended destination.
So on the one hand, it is ok for restrict the more efficient play style in game because it apparently makes the game to easy, but on the other hand it is perfectly fine, dare I say encouraged, to fork out an extra charge to easily skip 90 levels of content.
Skipping content that is irrelevant at max level = BAD. Restrict flying.
Skipping content that is irrelevant in terms age = GOOD. Charge 'em for it.