I'm sorry, and Naruto was doing what during those three years? Training? Thought so. Also, Naruto spent the vast majority of Shippuden actually hindered by the presence of Kurama inside him. Might I remind you he defeated Pain without Kurama's aid?
lol u must be kidding right, pain wasent even trying to kill naruto, when naruto was about to be sealed hinata saved him and then kurama raped pain. dont be saying naruto defeated pain all by himself when pain wasent even trying and when he got help from kurama and hinata