I say why not? This could be fun. ^^

Is it really so far of a stretch to have some underwater facility created by the Garlean Empire for Aikon research?

Hey, maybe Aikons come from the moon and they have a community there...

Or maybe they came from underground, or perhaps that is where they hide now.

Easy to fit all this into the lore of the world and make it interesting. I say go for it. But I also think they need to fix the current game first before we start thinking about all these extra goodies.