It didn't "break" wow, and at first I wasn't even aware of it or didn't want to acknowledge (after all it was something "new" and limited only to the new zones).
Over time it grew up until it became the standard pretty much everywhere.
I think I didn't become aware of the cons flying brought with it until patch 5.0. That's several years after flying was introduced.
Basically it ruins everything concerning open world activities (Questing, Levelling, Gathering etc), it heavily impacted world PVP (ok, this is not an issue with FFXIV) and had heavy negative consequences on world exploration, shaping and planning.
It made everything very difficult from a developer point of view, everything would be trivialized by the flying mount.
I swear I see the thing with very different eyes now, back then I couldn't see the concerns a very few people would expose about it.
Now I can clearly see how they were absolutely right.
Flying, with heavy limitations (only in certain parts of certain zones, only with certain requisites, for small amounts of times etc) can be fine, but "free" flying everywhere (in the new zones, for FFXIV) would likely be the same situation it has been in WoW =/