The Garlean Empire hasn't invaded the three starter cities has it? I think if the plan to create a more lively/dangerous/epic(I know cliche, sorry) tone or sense to Eorzea is this invasion or impending one then the zones would only make sense to be altered for the most part. Garlean experiments or attack strategies could wind up dis-shoveling and refacing the current zones in terms of mobs, monuments, and possibly(hopefully) geography. I don't actually think this will be the cause. I'm just pointing out how easy this can be to work into lore. If just one guy can do this:
http://www.youtube.com/watch?v=KVs4p...embedded#at=19
http://www.youtube.com/watch?v=z-m31...el_video_title
Then I'm not sure what the big deal would be, especially if they already have a starting template they can just improve upon. I realize the coding and implementation would add loads of time to the process...but still.