Madara was able to create a giant lotus that is far bigger than any Bijuu but that doesn't make it a god tree, its just a big plant that grows Zetsu's. Even if Madara grew a plant as big as the God Tree it wouldn't be the God Tree, the Juubi and Bijuu are the God Tree in different forms.
Another advantage that Naruto and Sasuke have ia that they both have more experience with Natural energy. Naruto in particular because he is a trained Sage. Madara's powers are largely stolen and copied, most of his powers aren't earned through hard work and experience the way Naruto and Sasuke's are. Madara may have far more abilities, battle experience, and power but Naruto and Sasuke had to get most of their powers the hard way and as a result they understand them in ways that Madara doesn't. Another major advantage that they have is teamwork. Madara is a beast of a man but he is still just one person he can't coordinate attacks in the way that Naruto and Sasuke can. We already saw how Naruto and Sasuke were able to coordinate their attacks and combined their abilities to create new ones of extreme power. Now that Naruto and Sasuke have had the experience of fighting against Obito and they have greater power than ever before they should be able to create techniques far more powerful than they could previously. If Naruto and Sasuke both complete their bloodlines Madara's advantage will be reduced dramatically. He will still have more battle experience and more jutsu but his only major advantage at that point will be the Juubi. Since Naruto has a personal and chakra connection to the Bijuu though, I suspect they will start to resist Madara's control. If Naruto can free the Bijuu, Madara will lose his advantage.
Even though most of the characters have been beaten down and can't fight in a meaningful way, like they did against Obito. They are still their to offer guidance and possible create openings for Naruto and Sasuke. All of the Kages are still alive and Orochimaru and his team are still there to help Sasuke + get the Zetsu's out of the picture and perhaps learn some secrets about Madara in the process. If Yamato is the one inside Spiral Zetsu, the allies might be able to free him and he might be able to take control of the Senju statue. There are still many options for ways that the allies can help create openings for Naruto and Sasuke.
Last but certainly not least, Naruto now has some kind of connection to Hagoromo, we still don't know what the extent of that connection is but that could help him in many ways. By learning the truth from Hagoromo himself Naruto finally knows things that even Madara hasn't learned. Naruto could use that knowledge to affect Madara. Naruto knows things about the Bijuu, Hagoromo's Sons, Hagoromo, the God Tree and the history of the world that Madara is missing. All of that information will probably be very important. As we have seen in many battles knowledge can be just as valuable as power, sometimes even more. As we saw with Itachi and Kabuto, Kabuto had designed his skill set to be perfect for defeating Itachi but he still lost in the end because Itachi was smarter and understood things that Kabuto didn't.