I think the term originally was meant for characters without flaws. Though people who write OC's in fanfiction sometimes write a Mary Sue/Gary Stu "in disguise" by giving them flaws that aren't really flaws, or aren't really important. So, with the right argument, you can prove many characters to be a Mary Sue/Gary Stu "in disguise". For example, Ichigo struggles sometimes, but he always wins, period. And he never had to change his way of thinking, and never had to grow as a character; all he has to do is say to himself "I'll win because I have to", and that's that. I don't think he's a real Gary Stu, though; for me, it fits that he's meant to be a weak character ("Hero", from Devil Survivor, is the best example I can think of), though the manga would probably be better if he was an interesting character instead.
Ichigo was the only character I really disliked in Bleach when I used to watch the anime (because he really gives off "Gary Stu" vibes). I don't dislike him as much now, I just see no reason to like him either (except for his interactions with Rukia). I also didn't like Ganju because he's ugly (how shallow I am), but he won points with me when he tried to face Byakuya. I never liked Aizen as a villain. I guess I more or less like all the other characters (even irritating ones like Orihime; I prefer to remember her few better moments).
Interesting enough, I didn't like Sui-Feng before her flashback; along with Ichigo and all the ugly characters, she's the only character I disliked at first sight.