No complaints about Deadpool.
But, I don't think it gets much more sue-ish than Wolverine's ridiculously complicated "mysterious origin" story. He's hundreds of years old, but he doesn't remember any of it, and he's been in
every war, oh and he's also a samurai for some reason (despite not being Japanese), and he's been experimented on to get a metal skeleton, and he's been a part of essentially,
every Marvel Superhero team (even though he's supposed to be a "loner"), even the
Fantastic Four.
He's a different kind of Mary Sue than Batman (more of an "Angsty Sue", though Batman might qualify too), but I would say he takes the cake over all.
Though, we are talking superheroes. I guess a little bit of Sue-ness is part of the genre. The real problem, I think is the way DC and Marvel over-promote these characters to pander to their fanbases. Does Batman really have to appear in every DC comic, and does Wolverine have to appear in every Marvel?