For someone with so many years of experience, kakuzu sure got decieved pretty easily. I remember the days when even seasoned chuunins would get kawaramied every which way by the most basic of jounins, and now a genin manages to mortally "punch" an akatsuki.
Naruto's always been capable of delivering the final blow to enemies, regardless of what level his rasengan was. It wasn't the power that was lacking before....