Honestly I can't really think of anyone I actually want to kill. Even characters I dislike have their place in the story. If I have to pick someone I pick Iggy koopa, I never liked that guy and he's not very important.
Well they walked on 4 legs in the older games and became bipedal in most of the newer ones. I think when they walk on 4 legs in the new games like in Galaxy it's just a reference to the old style of koopas. They walk on 2 legs except in space I guess. Maybe those are space koopas. :)