He said they improve as a Pair. He never said they were dead equal at all times. By feats RM Naruto would take EMS Sasuke without any effort. Forget the fact that he has Shin-Rikudo Mode and Biju Mode.
The last time they were equal was when Naruto only had Sage Mode and Sasuke had MS (and thats if Naruto isn't using the Kyuubi)
*Besides, That logic doesn't even work. Sasuke gained EMS when Naruto only had RM, So if Sasuke was "Equal" to RM Naruto (which is absolutely laughable to just think) then when Naruto got BM, Sasuke is just magically equal to him without getting stronger?
So far, Sage Naruto with prep could push EMS Sasuke to a Mid-High Diff Fight. Once the Kyuubi gets involved Naruto doesn't even have to try.