I am not against @TheSages456. I would love someone to actually provide manga scans where Naruto beats EMS Sasuke, when the god of Shinobi was aligned in power with an EMS user. This should also be a mirror, as Kishimoto is taking portions of characterization, abilities, and loyalties to build to a climax between the two characters.
Any Biju mode ability Naruto has is countered fairly easily by Sasuke's Amatersu variants, as Amatatersu by feats, has already bested a full-eight-tails beast. It would be absolute lunacy on part of the base to simple assume that Naruto would magically shrug off any enton, enton arrows, amatersau, or magatamas spams when the manga speaks against it.
The speed part is absolute non-sense, as is the A logic people keep employing to their benefit. Not only did A charge his armour to the max, but he used Body Flicker as well to barely evade a focused Amaterasu by a couple of centimeters. Naruto is faster than A in his fully charged Raiton armour Only, not the incorporation of an additional high-speed inducing technique, and he anticipated it coming as well. All these factors helped him dodge Amaterasu. When people actually show me Naruto evading A using body flicker and fully charged Raiton armour, then I will accept this point.
Another point is - let's theorize that Naruto can dodge it - is Enton Magatamas. These are literally a barrage of bullets, which even Zetsus - who have incredible sensing abilities according to the latest chapters - couldn't dodge. Naruto is faster than them, but how will a single individual dodge a shower of bullets? The Sharingan can easily see chakra, its distribution, disturbance etc, henceforth, clones distraction won't work against Sasuke, and they will be taken out easily.
Whenever he decides to throw a BD at him, he will get hit with a single flame, as an actual potent BD has a charge period, and this lapse can be easily manipulated by Sasuke to try out a number of instant abilities in his arsenal. Sasuke can also put Naruto under a temporary genjutsu, as Bee also scummed to it for several seconds before eight tails intervened to snap him out of it, albeit he is a perfect Jinchuriki as well. Not to mention Naruto's BM only lasts for 8 minutes, and his SM requires a large prep time, so that won't be feasible in such a scenario.
There are other factors as well, but these are the most popular ones used by Naruto-fans. This clearly shows that this whole 'omfg Naruto like totally roflstomps Sasuke' are only musings of a diehard, deluded fan.