What about the theories "Miqo'te was a race created by Allagan Empire, as one of those life mixing / crossbreeding / chimeras result."?
About how G'raha Tia has an Allagan eye, which means he descended (or probably created) from an Allagan ancestor?

Eh, one thing I'm still wondering about, the shinobis, the very first trash mobs in Syrcus Tower, are they human? or clones created by Allagan? Or were they from Doma?