Okay heres what I believe about the outcome of this battle:
I believe Nagato is the winner here, but not by the biggest margin. Madara has alot to offer in his arsenal against the mighty Uzumaki, but there are alot of things that Nagato has to nullify most of Madara's techniques. Here are key points I'd like to mention in my arguement:
1) Alot of you say, 2 meteors>Chibaku Tensei or that the 2 meteors are all that Madara would need. Clearly those of you who say this are misunderstood. Madara would not be stupid enough to use this technique unless he is bent on sacrificing himself as well. Because, if most of you can recall the manga, Madara was only able to resort to that attack because he was an EDO. If he was alive, he would die too and Im sure a man with enough battle experience as Madara would not be that reckless.
2)Madara's Mokuton is powerful of course. It took an army of full powered Naruto Bunshin's to halt. However, this does not nullify the fact that Nagato has these defensive capabilities: Preta Path to absorb (if he can), Shinra Tensei and the Asura machine capabilities to destroy the trees before it can reach him.
3)Madara's EMS techniques are his biggest asset to this battle due to his inexperience with the Rinnegan to its full capabilities. But, even with EMS we have seen a few things that would counter these powerful techniques under Nagato's arsenal.
---Amaterasu is vulnerable to Shinra Tensei. We see that in the battle with Itachi, Nagato was able to Shinra Tensei the flames away. Some may argue that he was hit and revived from being an Edo afterwards. However, remember that Nagato is being directly controlled by Kabuto. That hindered his natural reaction time to the attack, thus causing him to get hit. If it was Nagato all on his own then he would obviously have the ability to Shinra Tensei seeing it coming.
---Susanoo and the Gedo Mazo are matched up together. The only problem with Nagato is that the Gedo Mazo does not fully surround him like Susanoo would to Madara. So this part is clearly up to who can play their technique better.
---Tsukuyomi is the deadliest attack in Madara's arsenal. Because Rinnegan does not have any counter to genjutsu, at least not any we know of. So Tsukuyomi could allow Madara to win, if he was able to trap Nagato in it.
Now those are the main points but we also have, under Nagato's arsenal:
---Animal Summoning that are a pain in the ass. Cerebrus dogs will act as the biggest diversion or nuisance before Madara figures out how they work. Chameleon would be useless against EMS but another Rinnegan, Im not sure if Rinnegan Madara would be able to find Nagato. The Bird gives Nagato an aerial advantage, meaning that it could render most of the EMS genjutsu techniques out of play.
---Asura techniques are a powerful offense that could do alot of damage on its own.
---Preta path renders all of Madara's high level Katon jutsu out of play.
---Chibaku Tensei is Nagato's most fearsome weapon. Unlike the two meteors that Madara cannot use(unless he wants to die with Nagato), Chibaku Tensei will be death for Madara. Even if Madara uses Yasaka Magatama, it took a Rasenshuriken and TBB to take Chibaku Tensei down. We know that Madara only has 1/3 of the total power needed to destroy it because he doesnt have a Rasenshuriken nor TBB.
Also, Nagato would outlast Madara if it came down to it. Remember, Uzumakis have crazy chakra reserves while Uchihas have powerful chakra.
That is most of the facts that I need to state relating to this battle. I am not a Nagato fanboy and if you take a look at my avatar, you would know otherwise. This is my fair opinion on this battle and even if nobody agrees, Im still entitled to show others some evidence they can use to support either combatant.