Well, the basic point is that if he's well done, he isn't a Gary-Stu. The definition of a Gary-Stu is that he just doesn't work. He's inexplicably lucky or absurdly good at everything or related to ridiculously many canon characters just for the heck of it or is so good-looking that the author can't write a single paragraph about him without reminding the readers of it. He's always right and everybody loves him (unless said character is throughout the story shunned and portrayed to be a jackass). This has much more to do with how the character is written than the character himself. You can have a character who, by himself, seems slightly Stuish, but you write him realistically, without basing the whole world around his greatness, and thus he doesn't actually end up being a Gary-Stu.