Hmmm.
I honestly in the opinion that in Pain vs. Naruto fight, Naruto would have lost pretty badly if Kishi didn't throw so many favorable situations in his favor (like God Pain not in full power from the very beginning or Hinata interfering.)
It seems like sometimes he won his fights *not* because of his skills alone but due to his status as main character, if that makes any sense to you.
On that I don't think I disagree, the pain arc was fantastic though, best part of shippuden really.