I still think that Mwynn was a proto human and Bhunivelze was a robot she made to made find chaos, and it killed her when it seen chaos in her, then millions of years later when the robots made L'Cie (the new humans) they never thought robot were unnatural because they've always been there (they never call them robots in the game) But I still don't get why they had Crystals inside themselves, And why (this is from the sequels which kinda took the story off the rails a bit) Why Bunivelze slept in "Crystal" after he killed Mwynn, unless that was his Focus, but that would mean Focuses were around before the robots?
And I think Vanille has something to do with Etro and Mwynn. Her personality resembles Etro's "foolish" description, her special move is "death' also the final boss Orphan IV is vulnerable to Death, just like if Mwynn was the robots creator she would have that failsafe control over them, like how the Fal'Cie can control L'Cie. It would be awesome if that was like a kill a million years in the making :)
Okay I'll stop now...
Edit: Bunivelze couldn't see the chaos, so maybe it was the idea of the unknown he seen in the humans?