The difference between canon sue characters like Eragon and characters like Batman (who often get accused of being canon sues) is that:
a) Batman is allowed to have genuine flaws and failures b) Batman's victories are earned rather then handed on a silver platter because the writers can't bear to see him challenged in any way. c) Other heroic characters are allowed to second-guess and question his actions without being vilified for it.
I said it elsewhere and it bears reiterating - just because a character is very competent doesn't mean he or she is a sue (or stu)