Well, in FFTA, they were believed to be what held the world together but that proved false. On the other hand, Ivalice in FFTA is all about the power of belief from Marche and co. So wouldn't the crystals power be based on what Marche and the others believe them to be? Perhaps the crystals could also pertain to the powers of the laws and the judges? Maybe the palace created them as a way to amplify the power of the "Laws". Just some senseless musings...