People seem a bit confused about Naruto's SM limitations.
First of all, Naruto's 2 Rasenshuriken limit was due to maintaining his clones to refresh SM, which divides his chakra. In other words, if he was fighting "all out" rather than trying for a prolonged battle, Naruto has the option to use up to 6 Rasenshuriken.
Second, the same applies to the number of clones that SM Naruto can produce. Naruto was limited to creating a small number of clones in order to avoid disrupting the chakra of his other clones. If Naruto is going all out, he can create as many SM clones as he wants, he just won't have any gathering Natural Energy for him at the time.
Third, SM Naruto IS fast. There's no reason why he couldn't perform similar speed feats to SM Kabuto, who was easily able to dodge Susano'o arrows and Amaterasu with his sage reflexes. Naruto's speed feats include blitzing a Pain body from a fair distance away, and also handily wiping the floor with God Realm in Taijutsu.
All of that said, I think that MS Sasuke definitely has the upper hand in power in this fight. Naruto's only shot IS to fight a prolonged battle, which means he has to play very carefully with his Sage Mode. I believe that Naruto can probably enter Sage Mode by having a clone hide and gather Natural Energy, and would probably have to stall using Kyuubi Chakra to create a large number of clones. Sasuke's Susano'o is hard for Naruto to deal with.
However, Sasuke has to end the battle quickly, and can't play into Naruto's stall strategy. His Susano'o isn't very mobile with just MS, and he can't use many MS jutsu before exhausting his eyes. Naruto has far more power than Danzou; Danzou attacked primarily using fairly weak jutsu, and only pressured Sasuke due to his stamina and his ability to bait Sasuke into wasting chakra on MS techniques. Naruto is superior in terms of stamina and baiting techniques, so long as Naruto uses his clones wisely and takes advantage of both his Kyuubi Chakra and his Sage Chakra.
I think that Naruto unwittingly handicapped himself against Pain by relying solely on Sage Chakra from the get-go and only utilizing Kyuubi Chakra once his Sage Jutsu ran out. Obviously that fight was meant to showcase his Sage Mode, since it was being used for the first time. When Naruto first ran out of Sage Chakra and had to be refreshed, he was forced to stall in Base Mode until his reverse summoning was completed, but he could easily have pressed his advantage if he created a small Kyuubi Cloak. The only reason he didn't was because, at the time, he believed using Kyuubi chakra was a weakness, and didn't trust himself to control it. In the end, the Kyuubi chakra saved his ass, but that was only after he lost control.
SM Naruto's true power should be measured taking into account the amount of Kyuubi Chakra that he could use at the time while maintaining control; Naruto can easily handle 1-2 tails worth, and can still maintain control over up to 3.
There are arguments that support Sasuke being able to suppress Naruto's Kyuubi Chakra with Genjutsu, just like he did when they first met again in Part 2. It's hard to say exactly how that would play out if Naruto fought Sasuke again and was aware of that risk. Obviously Sasuke never tried to suppress another Jinchuuriki's Bijuu again, either while losing against Bee or while fighting Naruto in VotE2.