Maybe this thread was better on Lore section.

But, going to the theme, I think Allagan are not death. Probably they have a hiden place. And hiden city or something, were they just seclude themselves, and isolated form the world outside. A hiden place I want to visit. Looking at Azys Lla, there is no one Allagan there, but, the place is mostly intact (maybe because robots still working), but all machines works an the place is still working. So, that's mean, not all the Allagan stuff are just ruins. The Coil is also intact and at full funcionality. So, maybe there are a place where the Allagan still live, even in another dimenssion.

The story of the game problably will make us know, with the help of allagan survivors, to undestand what is Zodiark, what ascians want, and find a way to fight Zodiark and his menace.