To be honest, in the show, Naruto would win barely since the show is called "Naruto." No chance in hell Kishi would let Naruto lose.
Realisticly though, Naruto is horribly weak against Genjutsu, which Itachi is a master at. This could be Itachi's win condition, since Naruto can keep up with Itachi's ninjutsu and taijutsu in Sage mode. And it isn't Naruto's lack of brains that would make him lose. Naruto has proven himself smart enough on the battlefield now in the ways he has beaten the 3rd Raikage and Pain.
My reasoning in Naruto's loss would be because of Itachi's Tskyomi. Im more than certain that Naruto can get around amaterasu and can find some way around Susanoo. If Naruto gets trapped in a genjutsu, he is done for.
Now in Naruto's defense, we do not know how Sage Mode is with Genjutsu since he never has been put in one while in Sage Mode. Who knows? He might be able to sense a disturbance in the nature chakra or something and find a way to break it.
Basically, I don't think we have enough information at the moment to make a full decision, but I'm leaning towards Itachi for the time being.
EDIT: And also the fact of the matter people is Naruto has the Kyuubi, and no matter what form Naruto is in, the Kyuubi will come to the rescue if Naruto is in danger of dying. So stop crying "Wah Nagato would have won if it wasn't for the kyuubi." Yes that is true, but you crying about it won't change the fact that Pain lost. It is a massive tool in Naruto's arsenal, and he is going to use it in a fight, especially against someone like Itachi.