Well, being "exceptional" is one thing, but being flawless is something completely different. I agree that the best characters are exceptional, but flawless characters are difficult to take seriously, and tend to be quite boring.
Take Frodo Baggins, Thomas Covenant, Malta Vestrit, Jon Snow, Miles Vorkosigan, Sherlock Holmes or any of the countless prominent characters from fiction of any genre -- they are all quite exceptional, but also significantly flawed in one or many ways. I didn't see any prominent flaws in Kvothe, which made him really boring and uninteresting; now, as someone else mentioned, he is an unreliable narrator of his own life story, and it is quite possible that in later books it will turn out that a lot if it was a lie and his flaws will be revealed, but by then I have long lost my interest and I don't think I'll ever get that far. I do enjoy a good twist in the story, but the story up to that point needs to be interesting on its own; Usual Suspects wouldn't work at all if Verbal Kint was a flawless character.