This may be a silly idea, but it's been bounching around in my head for a while (since I've been playing the GBA versions of a lot of the older FFs), but I'll mention it anyway: What about the crystals? Originally it seems they were simply to hold Ivalice together, the threads of desire. Yet the people of Ivalice believed them to have been constructed by the palace inside the seams, and that their magic was beneficial to Ivalice. Could there have been another purpose to their existence?

Anyway, plot's coming along fairly nicely, but with Burning Crusade just out, it might take me a little while to get a good update. Sorry.