I know it uses the Aern model and has the Dragoon job, but I mean, why was it jailed? (it appears when you kill all the jailers of the different virtues, so I assume it's being held captive) Where did it come from? What function does it serve? How does it fit into the world? Is it the combined virtue of the Zilart people that they removed somehow, similar to removing the emptiness from themselves in the Chamber of Eventide? Or maybe is it the Zilart Emperor after he rid himself of emptiness (this doesn't really make sense as the other Zilart are the quasilumins, not the Aerns)?
I'm just grasping for answers due to the limited lore provided in the game (really, most of the endgame bosses have very little actual in-game lore unless they're part of the missions, and they deserve more.)
Why are Kirin and the other 'sky gods' on Tu'Lia? Who are they in Vana'diel's mythology (not earth mythology)... they seem like animals that have attained 'god-hood' like the Terrestrial Avatars, but they're not avatars are they?...
Who or what are the "Crystal Warriors" (I mean the Ark Angels) really?
We get at least two stories of what they are during the game and neither held more authority than the other, in my opinion.
Other crazy thoughts:
Phoenix is the fiery bird of resurrection... why can't it revive itself with its own innate power?
Are Dark Ixion and the Auroral Alicorn avatars? They seem to do similar things as the Cait Siths, only they don't talk.
If Pandemonium Warden is supposed to be guarding the gates to the underworld, it's doing a really bad job, letting the Einherjar and Odin out so often. Does it work for Odin? If it's not keeping things IN the underworld, is it trying to keep us out?
What does the Emptiness do to areas that it has come into contact with? Just how destructive is it, because apparently, in the Far East, when people were overcome by the Emptiness, they fell into a slumber and other people were able to get them and use them for sacrifices to try to revive Phoenix, so it sounds like the land around them was left "untouched" and only the people were affected. The only other contact we've had with the emptiness is Selh'teus and his control of it in the Crags, which may not be indicative of what the Emptiness does on its own.