Well, going by the spirit of the OP I think we mean "badass" attitude wise, not in terms of their raw power. For example the OP mentions in Rurouni Kenshin that "Saito" is a bigger badass than Kenshin, yet he is proportionatly a weaker character, I'm not even sure if I'd put him in the top 5 for that series (sadly the names of most of them elude me, I need to rewatch it eventually). Attitude wise though, yes... he's a badass.
The thing is that the "Badass attitude" generally works better as a supporting character because the general qualities that make someone a badass are not traditionally heroic. Such a character works well backing up a character with a more heroic outlook, and perhaps doing the dirty work for them when it needs to be done to move the story along. Typically when such a character becomes truely heroic themselves, oftentimes by being changed by the protaganist, the story ends or the character dies off so you never really see the results of the change which would portray them very differantly.
To use an anime (which other people have referanced) as an example, look at Trigun. Vash is generally the antithesis of a Badass, sometimes he acts the part, but in the end the guy is a peacenik who can't kill. His "parner" Wolfwood on the other hand *IS* a Badass and saves the hero on several occasions by doing what he cannot do, for example finishing off a certain samurai-type guy. Later it's arguably Vash rubbing off on him (to an extent) that leads to his death, and the timing of his death also figures into the climax of the series because the hero doesn't have Wolfwood around as an "easy out" to clean up the mess so the hero can maintain his principles. Understanding that is part of what is supposed to make it dramatic.
In cases where you have a protaganist who is a Badass, typically your moving away from real "heroic fantasy" and into the realm of "Dark Fantasy" and so on. For example Kratos gets away being what he is largely by being an anti-hero at the best, and sometimes an outright villain.
One important exception though is comedy. Something like Dragonball Z gets away with it by being a massive satire... while fairly consistant within itself, it's intended to be an absurdist comedy. The same can also be said of things like the video game "Kenka Bancho" which basically makes fun of the entire idea of being a Badass, while at the same time worshipping it oddly enough. The old movie "Big Trouble In Little China" was also a giant send up of the entire idea of the badass anti-hero protaganist, which is again why it worked (though the joke was that Kurt Russel failed at pretty much every badass thing he tried to do except for one...)