This probably would have been resolved if the beastman races had been playable from the start, as they really are the closest thing you have to a constant and true antagonist.
The main concern with something like this is the placement, and how much of the content would be involved. It works in single player RPGs because they're temporary places you can access due to the story. You went into Zozo to find Tina/Terra and later in order to get into Mt. Zozo to recruit Cyan. You went into Vector to deal with the magitech research facility and as part of the events that lead to the end of the world (of balance). Zozo in particular was incidental in the greater scheme of things. Vector was involved when the game hit the part of the story it was relevant to and then vanished.There was something rich in the experience of being in the areas like Zozo, and Vector. That feeling of risk of exposure, the near-tangible tension in the air as you tried to complete your quest, or even just explore what it was like there.
FFXIV provides a unique opportunity to resurrect this great area concept rich with possible quests. Perhaps we can explore the neighboring country of Al Mhingo under Imperial Occupation and assist the resistance movement, witnessing first hand the way Garleans try to convert it's territories.
Maybe we can go straight to the Garlean capital and have a chance meeting with the Emperor himself, before fleeing through their back factorys in an attempt to escape their clutches.
These are type of areas ripe with memorable adventure and story that we could experience first hand, instead of reading in an article. I hope Yoshida and crew consider this for possible expansions to the 2.0 version of FFXIV if they're not already there.
IMO, for this to work in an MMO you'd need to do one of two things. You either have it as part of a mission storyline where you're effectively locked in that zone up to a certain point (the way Vashj'ir was done), or you make it part of a bigger storyline where you're tasked with infiltrating enemy ranks and completing quest objectives up to a certain point where you do something big to sabotage the enemy operations and go back to normal (like it was done in Mt. Hyjal).