I don't know about this...

[saber_alter]

-snip-

they're cut off from their main supply of resources in the air. no food, water, or basic living supplies means no sustaining boime. those creatures on Azys Lla aren't that edible after all. And with the main empire effectively gone, no reason to continue something that lacks purpose.
Aether isn't like mako, (the most it gave us was a headache, but a more extreme case is that it completely froze over coerthas)

[Waffilicious]

-snip-

If its like that then where does the 2/3rds of survivors go? most of the farms are always away from the main city if it goes by our logic, plus it is said the earthquake shook all of eorzea but eorzea is but a continent. did they spread? went underground? more flying colonies? space? Only future expansions will tell us (i really wanna know every era).

And aether can be toxic, example one all the zombies from pharos sirius they are aether poisoned pirates not tempered by leviathan. In cnj story if i remember correctly the girl went down with a fever for having too much aether inside herself. So it can be a cause, maybe not but i like my speculation :P

[Fenral]

they're cut off from their main supply of resources in the air. no food, water, or basic living supplies means no sustaining boime. those creatures on Azys Lla aren't that edible after all. And with the main empire effectively gone, no reason to continue something that lacks purpose.

Except one of the islands on the western edge looks like a residential complex, complete with garden, and the Delta Quadrant has no shortage of water. The facility has been left running on auto-pilot, but not for inability to sustain life. All the monsters running about only escaped for lack of maintenance after it was abandoned, near as I can tell from the side quests.

So what the seven hells happened? I don't want to doubt the "most were wiped out, but some survived" explanation, but it's kinda lacking in about a million different ways now that we know Azys Lla not only exists, but is still quite operational.