I said it once and Ill say it agian; Each person in the series has advantages and disavantages when it comes to their abilities. Take the 3rd Rikage. He has high stamina, speed, and insane lighting techs. However, if he battled lets say Itachi, a genjitsu master, well he would probally loose because while he is gifted physically, mentally he is probally the most varniable. How lets take another strong character kakashi. He has tons of ninjitsu, tiejitsu, and some genjitsu techs. He is smart and he also has a MS technique. however, his problems are his techniques are not as powerful as most ninja at his lv. and his stamina and chakara level is terrible. His true strenght is in a group where he can combo his abilities with those of his comrades. But, indivisually he is not so great.
In Naruto's case he has stamina, physical power, a single (increasingly versitile) strong ninjitsu, tons of Chakara, the ability to think on his feet, summon frongs, and the ability to have deadly combos. However, his genjitsu prowess is not great and as long as him and the fox don't see eye to eye, he will continue to be massivly varniable. In addition he is predictable and if you had the ability to supress the foxes' power and have high defense (like sasuke) then I think that Naruto will have a very hard time beating this type of person.