Slightly obscure, slightly unliked, and slightly alternative (to the major mascots)? I can only think of one character:
She's quite possibly Nintendo's greatest character in several years. Yeah, she's annoying when you first meet her; even I wanted to strangle her. But how she changes as TP progresses is one of the most beautiful things in gaming. That, and her personality screams "mascot."
If we're talking about characters who appear in more than one game, then I'd have to go with Travis Touchdown.
I picked Travis mainly because he's really obscure, and not an ordinary video game character. He's a nerd, and he's proud of it. That, and he could be a decent representative for gaming, if he weren't so bloodthirsty and arrogant.