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It's always been my personal belief that the biggest badass in anything is never the main character. He/she may be a main character, but never the main character. To run down examples off the top of my head --
Rurouni Kenshin - Hajime Saito,
Dragon Ball Z - Heavily debatable, but for being consistently badass, gonna have to go with Vegeta,
Yu-Gi-Oh! - Seto Kaiba,
Full Metal Alchemist - Again heavily debatable, but I'm going with Pride/Fuhrer King Bradley
EDIT: Syphon Filter - Anton Girdeux
Mega Man - Proto Man
Kirby - Meta Knight
Zelda - Sheik
Batman - Deadshot
Spider Man - Venom (or Carnage)
--
just to name a few.
Now I've been trying to think of exceptions for this rule, but I'm drawing a blank. How about you guy/gals?
Also I understand this is all opinion based, so please no flaming.
EDIT: OP has been edited so all the examples aren't nothing but anime. That was a tad narrow-mined of me. I'd also like to add that this rule has been extensively shot down, but new responses are still welcome.