The only real twist with Dysely was the nature of his evil. I pretty much thought he was at least a l'Cie when I first saw him and thus a bitch to the Fal'Cie so I was a bit surprised he turned out to be Fal'Cie, but not at all surprised that he was evil.

I'm pretty much with Raistlin on the game's plot. I also agree with arcanedude34 that FF has never exactly been good about hiding main villains in the series.