Shikamaru wins this, no contest.

Yeah, Naruto does have some clever tricks up his sleeve, but at what cost? Everytime he fights, he wins through a sudden comeback. Whereas, everything we've seen of Shikamaru, has him in control of the match. Add to the fact that he doesn't rely so much on the jutsu to win, but natural surroundings. That, my friends, is what it means to be a truly skilled ninja.