Theres a thing called anima

[Charismatic]

Every possible change ever effects the game as a whole, but is it necessarily a negative impact? Well, I certainly don't think so.
People getting places faster doesn't suddenly make the game worse... or shouldn't if the game is well-designed. Unless of course you're on a specific quest where for some reason that is the point of the quest and all they'd need to do is restrict airship/anima usage while the quest is active. Simple.

[I personally don't believe there should even be those kinds of quests unless it's something like smuggling stuff on the airship (with there actually being some skill-based method of success) or a race or something like that. Something that requires focus/concentration/skill rather than just walking just to walk or riding an airship just to do it.]