In your opinion, what comicbook superhero (or superhero group) just doesn't belong in their company's shared universe?
I'd call DC's Batman. He's at his best when he's closest to his classical roots as a noir-ish character with tech just a little better than contemporary state of the art. Trying to make him fit in a world with a Justice League requires either converting him into Iron Man, or requires making him intelligent/competent to the point of siphoning all the challenge out of his existence.