At the start of the XIII project (2003 or so), Kazushige Nojima came up with a basic mythology, which has been loosely applied to all the "Fabula Nova Crystallis" stories.
So yeah, Pulse, l'Cie, and crystals have been worked in.
He should worked on it longer... the idea of getting fucked by both completing/failing your mission sucks moose balls. :(
Cocoon looks cool though...