In all honesty, I didn't like Snake in Brawl either. But he still fit better in that game than Bayonetta in this game.
First of all, Brawl was actually rated T and not E. Another thing is, Snake doesn't do a real choke hold. If anything, he's more holding his foe's head back by the chin; and not back nearly far enough to snap their necks. There WAS actually an unused, realistic choke hold animation planned, but it got dropped. Guess why.
Besides, just the characters themselves, from their respective games, are not at all the same. Snake is a soldier. He fights in wars, but only in wars, and he'd rather avoid conflict anyway and usually prefers stealth and sabotage. Bayonetta is...a witch whose clothes disappear. When she uses black magic. To summon demons.
Yeah, I know, blah blah blah, alternate universe with fictional pseudoreligion. I know, yack yack yack, they censored the nudity. But...come on. Seriously. Which one of those people would you imagine being more likely to hang out with Mario and Link?
Either way, though, that's STILL not the main reason I'm not happy for her announcement. The main reason is that she looks completely frustrating and unfun to fight against.