My real antagonist of my series doesn't even show up until the second book, but still manages to be accounted for most, if not all, of the complications in the first.
The character set up to look like the main antagonist is actually a neurotic mouthpiece--and another "villain", introduced early in the book as something of an abettor to the real villain of the story, and appearing near the end of the first book, is made out to be a more apt adversary; but this perception is radically changed about halfway through the series when his involvement with the MC's parents is revealed.
He turns out to be one of the most interesting, redeemable, multi-faceted characters in the entire series. I would even go so far as to say I prefer him to my MC.
But I made an effort to make the Big Bad different from most of my other villains. He's not described as exceptionally handsome or charming (though I'm not saying he can't be percieved that way).
He's untaunting, and almost has a very wise, mentor-ish feel to him. He never loses his temper, and thinks everything through. I'm not really sure what to make of him, or what it is about him that makes me uneasy--but he manages.
The villain in my short is a giant-voodoo-walking-stick-bug-thing with highbeams for eyes and violin bows for legs that lives in a spider hole-thing.
And he eats people.
There's also Thom, but no matter how much he pretends not to care, he still does.