The only two that comes to my mind are Wario and Donkey Kong, who was the main villian in Super Mario Land 2 and Mario and Wario. Donkey Kong is the main villian in the Donkey kong game and the Mario vs. Donkey Kong franchise, but aside from that how many villians in the Mario universe have been the main villian in more than one game in the Mario series. Fawful doesn't count he wasn't the main villian in Superstar saga.  Most other villians are one time usually.

I'm gonna go ahead and say Hitler

Master Hand?

Dr. Wiley is an obvious example.
Edit: sorry, missed the Mario universe part.

I was talking about Mario games, the post thing is too short for me to say my whole thing.

Man Mario should have put a gun to Bowsers head and pulled the trigger like four games ago.  I know that is what I would have did I would have been tired of his nonsense and trying to kidnap my girl all the time.

It's the same thing all over aint it.

" I'm gonna go ahead and say Hitler "

Ganon, maybe?
 
Edit: Oh yeah! And Andross!
 
Edit 2: Oh crap! I was thinkin' of Nintendo in general. Not specifically Mario. Whoops!

Nah he's always in the shadows.

Heaven help us all. Beside he did return already, twice.

Cobra commander,
 
Dr. Cortex (crash bandicoot)

The Koopa kids!