I think the greatest villain was everyone's lack of experience which made combat take hours which made our sessions always end with very little plot progress.
This, pretty much. I can't even remember much about the plot in the group I played with in college. I ran a campaign in high school based very, very loosely on SMRPG, and thought my anti-hero/villain guy was super neato cool, but in retrospect he was a Mary Sue. >_> The players decided to fight him way before I wanted them to and despite the best hints I could muster to surrender, and got beat the hell down. We didn't last long after that as a group D:
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~Tommeri Uranius Bombaldi the Fourth, esq.
(aka not Krakenprophet)