The whole point of the last segment was to level their abilities better.
Naruto needed to lose power before getting a power up so as to not completely overshadow Sasuke. Up until that point, Naruto had only progressed further and further, while Sasuke kind of stagnated after leaving Orochimaru and killing his brother. This left a huge gap between their power levels; one that Sasuke just couldn't overcome.
Therefore, Kishi had Madara extract the Nine Tails from Naruto, thus weakening him significantly, while Sasuke really didn't lose anything in his death. At this point, Naruto was brought to a level that Kishi likely deemed relatively equal. The two still needed to be able to defeat Madara, and thus were each given half of the So6P's abilities. This was only meant to signify their significance in the story and make them powerful enough to defeat Madara; They are still evenly matched in terms of power level, though.
Naruto has two things going for him, though, that should serve to make him better than Sasuke. First, Sasuke is still a rogue ninja. Just a little while ago, the Five Nations considered him a member of the Akatsuki, and everybody, except his small team, saw him as an enemy. This really doesn't matter in a one on one fight, but seeing as the entire theme of the series is teamwork, this could play a role in their inevitable showdown. Furthermore, Naruto also has all of the Tailed Beasts (and their abilities). This may or may not be part of the S06P's power up, but this gives Naruto access to all of their unique chakra and abilities. We have already seen him use magma, but he should also have access to sand, slime, acid, etc. Furthermore, Naruto should be invulnerable to Genjutsu now. Jinchuriki were already considered immune to genjutsu since they have their tailed beasts, and now Naruto has nine tailed beasts to help him. Finally, the tailed beasts seem to have memories going back to the time that they were originally separated from the Juubi. Additionally, they have likely fought against nearly every notable ability in the series. This means that Naruto literally has generations of information and experience at his fingertips.
In contrast, Sasuke just has his new eye. We still don't know what it lets him do, but it better be more than just a combined Sharingan-Rinnegan to ensure that Naruto and Sasuke's powers are still even. Perhaps the mind-reading capabilities and mind control (like the Inoichi clan), like Zabuza originally thought the Sharingan had.