All I have to say is fusion of Bijuu Mode and Sage Mode like he did when talking to Nagato. I know that Kishi did not show us that for nothing.
But disregarding something that hasn't happened yet I still say that Naruto still has a chance against Madara. The only real reason that Obito has been so difficult is because of his MS Space/Time Jutsu. Plus that fan seems to have some kind of special ability if it is able to block a MiniTBB, although I doubt it could do the same against a full scale TBB.
Now I am going to go step by step through everything:
Rinnegan - Yes It is going to be a challenge but it is not like Naruto and Kakashi have not gone up against it already and don't know how to defend themselves against it. I believe the most challenging thing is fighting two users with a Rinnegan. But with Kakashi & Kurama on his side I don't really see Madara & Obito outsmarting the hell out of them. Plus now that we know that Naruto can make Sage Clones it would not be as easy for Madara to just walk over and take it right out of him. We all know that Kurama has a personal vendetta against Madara so strong that he was willing to give Naruto his ful power and eventually become friends with Naruto. So now that Madara is not able to just summon Kurama I would like to see what Kurama would contribute to the fight other than his Chakra because currently he is the oldest, wisest, and smartest being in the Manga right now..
Mokouton- Wood release yes is strong but you all also haev to remember that Naruto has all of Kurama's powers. Why he hasn't been using it is beyond me. I would love to see Naruto use the Tailed Beast Shockwave which would knock back or vaporize all the wood that Madara would create. Not saying that he could just spam the hell out of it but he does have a defense against it. Plus he could also use Big Ball Rasengan.
Tsukuyomi- As one user said he cannot be put under Genjutsu because of Kurama
Perfect Susanoo- Yes it is very powerful but we have not seen nothing other than him destroying a mountain. If I am not mistaken I remember that Kurama flattens mountain just with a tail so what he did before is not that impressive. So as far as who would win between them two no one can really say because both Naruto and Madara can create clones who can both have a Kurama & PS tied to each one.
Now I am not going to name anything that Naruto can do because without Madara being sealed none of it matters as of right now. He could destroy him time and time again and the only that that will happen is that Madara would just regenerate. Also it will be a difficult fight for Naruto because he is definitely is not as experienced as Madara, he can't regenerate, he doesn't have unlimited chakra, & no one knows the extent of what that fan can do.
But I can tell you what Naruto does have that he has going for him and that is:
Fusion of BM &SM
That Jutsu
IIIIIIIIIIIIF he ever learns FTG
IIIIIIIIIIIIF he got power from the other 6 Bijuu
His very strang and stronger connection to Rikudo