Simply the difference between a recurring villain and a climactic villain. If you think one is more threatening and "real" than the other, more power to ya. It is really an opinion kinda thing.
And, really, what about Charlie Ho-Tep? He was not only powerful, he was very sneaky and he was very threatening. He was the reason of Sam clone outbreak, which made Skunkape suck his ape thumb, and he tried to summon a toddler elder (?) god. I think you forgot these little factoids.
Also what about Maxzilla? He was very climactic (him being one of the two main characters), very threatening, and as the basis of sheer power output, he is clearly the winner. I don't know... Skunkape himself was overwhelmed by the disasters that he unintentionally caused, you know, most of which are actually the disasters that Charlie Ho-Tep INTENTIONALLY caused over the span of centuries...
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