Minato can unseal the fox, causing Naruto's instant death U_U and Naruto can't harm him because of the FTG. To beat Minato one needs to land a fatal blow.
Eh.. In Kishi's head, Naruto has surpassed his daddy.
But in logic, Minato wins. Just too much experience to overcome there. Battle smarts and some pretty perceptive abilities. But it'd be a nice little tilt, I say Naruto lands a few good ones.