A few things:
Where did Zetsu say that Naruto is stronger than Sasuke?
Pain technically defeated SM Naruto.
Sasuke's MS Susanoo would defeat a SM Naruto.
We have yet to see what Sasuke can do with EMS but Naruto has yet to display anything to counter Ama in BM.
As others have said before, both characters are kept at about the same power level.
Naruto beat Kakuzu and Sasuke beat Deidara.
Naruto beat Pain (with intel and a Pain handicapped most of the fight) and Sasuke beat Itachi (with Itachi handicapped and planning to die in the end)
MS Sasuke with Susanoo is about equal to KCM Naruto
EMS Sasuke complete Susanoo (with armor) is about equal to current BM Naruto (with only yang half of Kurama's chakra)
These are the trends that Kishi has showed in the manga. If you fail to ignore this then you are being biased. I can give arguments on how each character can beat each other at different points in the manga, even in the current arc.
Of course Naruto will eventually beat Sasuke, he is the main protagonist. He is the namesake of the manga. In the end he will be on top, but it isn't going to be an overwhelming difference between himself and Sasuke. Naruto will when by guts, like he always has.