As I showed in the FF Villain Accomplishment thread, Yu Yevon is nothing more than a mechanical force, endlessly repeating the Summoning and dreaming with no will of his own. Thus, I can't consider him a "villain" because a villain knowingly commits some sort of violent act and can decide whether or not he does it. Yevon can not do that and apparently hasn't been able to for quite some time.
I'd say the Yevon faith is more to blame than anything for the state Spira is in.