I don't get why people say,
MS Sasuke = SM Naruto, but EMS Sasuke > SM Naruto?
How does that even make sense, the only real difference between MS and EMS is that Sasuke no longer runs the risk of going blind while fighting against Naruto.
It's also been theorized that the user who receives EMS get's a new ability, I'm not sure if this is true. In any case SM Naruto is faster, stronger, and can out last Sasuke in a fight.
Naruto stood toe to toe with Pain a master of the rinnegan(yes I know Pain had a handicap) but with such limited info on Pain he still proved his worth in that fight IMO.
I think Naruto would have a tough ass time beating EMS Sasuke with just sage mode, but he could definitely still win, especially if the fight was drawn out. Sasuke may have Susanoo' and Amaterasu, but these skills use up a lot of chakra and aren't the most efficient offensive abilities. As soon as Naruto turns on the heat and starts forcing Sasuke to defend using Susanoo' more he'll burn through his chakra quick.
The beautiful thing about sage mode is that it practically gives the user an unlimited amount of chakra. We know Naruto can dodge the susanoo' arrow as we've seen Kabuto dodge it, we also know Naruto has Kyuubi to disrupt any genjutsu Sasuke tries to pull out. Amateratsu can be dodged because in Sasuke's fight with Itachi, Sasuke was able to dodge them, and I'm pretty sure SM Naruto>Base Sasuke speed.
Chidori is countered by rasenshurikan, and any fire style jutsu can be countered via ma or pa, or any other toad summoning Naruto decides to use.