Reading a lot of information, especially information from issue 520 (I've read some of the spoilers), I'm starting to put together a theory about Madara. I'm marking this post as a SPOILER because I mention some things from the spoiler for 520. Don't read this if you are trying to be surprised by 520.
What do we know about Tobirama? He was extremely powerful. He was a master of water style and space/time jutsus. He also apparently conceived of the most evil jutsu in the entire series: Edo Tensei, the ability to trap a dead soul into a body by killing a sacrifice. When he become Hokage, Tobirama created the police force to segregate the Uchiha from the rest of the village. Tobirama sacrificed himself during the second great ninja war to save his squad. We never see him die, and none of the characters seem to have seen it either. He was apparently the most powerful ninja alive at the time of his death.
What do we know about Madara? He was an extemely powerful Uchiha who frequently fought Hashirama, because the two of them were the tops of their clans. He apparently died in battle against Hashirama, with many witnesses. But he claims otherwise: Instead of dieing he somehow gained Hashirama's power during the battle and eventually learned Izanagi, Gained the rinnegan to give to Nagato, grew some of Hashirama's cells for the big flower thing, and used it to create a gigantic army of Zetsu clones.
Much later, Orochimaru learns the secrets of Edo Tensei and "perfects" it before being merged with Kabuto. Keep in mind that only Kabuto called in "perfect", and Kabuto is evil. Tobirama would not have called Kabuto's version of Edo Tensei "perfect". In fact, I don't think the two are the same jutsu.
If Tobirama was a good guy, it seems weird that he would have created the most evil jutsu. I think it's pretty unlikely that Tobirama would have ever attempted it or practiced it, because people would get upset if the Hokage were killing sacrifices to test a new Jutsu. That's an evil kind of thing and not something the Hokage would be able to do. Tobirama loved his people, loved his village, sacrificed himself for others, and would not have used something evil like Edo Tensei. He probably wouldn't even have thought about it, at least not the way Orochimaru used it.
Orochimaru on the other hand is evil. He can do evil things like kill people for Edo Tensei. We frequently see him sacrifice the people around him for his personal gain. We frequently see him kill people for experiments, and he would have had no problem doing that for Edo Tensei. Kabuto claims he did many experiments with it.
Let's assume that Tobirama developed a technique that allowed him to communicate with the souls of dead people, and maybe gain their power and learn techniques from those souls, temporarily. This technique would have been very helpful, but it would have been limited because Tobirama didn't want to hurt anybody while doing it. Even in this limited state, Tobirama would have appeared to be the most powerful ninja in the world because he could use the combined powers of other ninja who had already died. Orochimaru would have seen the limitations as "imperfections" and would have been eager to "perfect" the technique. He wouldn't have worried about killing people in his experiments until he found a version that he could use.
Tobirama develops a technique that helps give him power and knowledge. It allows him to use the souls of dead friends to help him protect the village. This is perfectly reasonable, and something a Hokage might do. It is a little dark, but isn't evil and doesn't require sacrifice. Plus, it helps people communicate with their dead loved ones, and bring peace to souls killed in battle. Orochimaru turned it evil, but removed some of the limitations from it.
This assumption is perfectly in line with everything we know about these two characters: Tobirama loves people and forms strong bonds with them which last after death. Orochimaru does not value people, and is willing to sacrifice their lives for his experiments and use their souls as tools to help increase his power.
Now, enter Madara/Toby. This character does not appear to have any EMS techniques like the real Madara was supposed to have. He also was supposed to have died in the Valley of the End, but is still alive. Itachi says he is just a shell of his former self. He now has Izanagi, which appears to require both Uchiha and Senju essence in order to perform it.
What if Madara is an Edo Tensei soul trapped in the living body of Tobirama? What if Madara is a "shell of his former self" because he was created using the "imperfect" form of Edo Tensei that Tobirama created?
Tobirama is in the second ninja war and his team is surrounded. He sends the rest of his team off and prepares to engage 20 ninja by himself. He's fighting and dieing, so he uses one last Jutsu: Edo Tensei. He summons the soul of a powerful warrior into himself so he can give his friends a few more minutes to escape. That powerful warrior is Madara. Madara's soul gives Tobirama more chakra and he can continue the fight, eventually defeating all his enemies.
Tobirama would have used space/time jutsus in the battle, so Madara's soul would have witnessed those and learned them. Tobirama would probably not have used Edo Tensei again, so Madara's soul would not have seen it and would not know it.
Kabuto's Edo Tensei keeps all the abilities of the soul he summons: Itachi still has his MS, Nagato still has his rinnegan, etc. The souls that Kabuto summons are also invincible. Either of these things could change as the limitations in Tobirama's version. Maybe the summoned madara had sharingan but not EMS. Maybe he could live for a long time but was not completely invulnerable
Tobirama uses almost all his chakra and cannot control the soul of Madara Uchiha any more. He dies, and Madara's soul takes over his body. Now we have "Madara" with the body of the Senju and the spirit of the Uchiha, with Sharingan (but not MS), with powerful space/time jutsu like Tobirama had, but limited in power because of the "incomplete" Edo Tensei that Tobirama used. He's probably not indestructable like Kabuto's version, but he has been alive for a very long time without dieing. He is now a shell of his former self who needs to use the power of the Sage of Six paths to make himself whole again. In other words, he needs to create a real body for himself, and move his soul back into a real Uchiha body where he will gain all of his old powers again.
Madara's "real" body could not be in the coffin, because Madara's soul is in Tobirama and cannot be summoned from there. Tobirama could not be in the coffin either, because he cannot be summoned again, because he was sealed by Hiruzen. This theory does not explain who was in that damn coffin.
Tell me what do you think, guys? That theory may best than Obito's theory.
. MS spawns in a person during a time of extreme distress and the abilities one spawns from that experience are 100% unique to that person and his MS. When itachi died, he implanted ALL of his abilities into sasuke and when he developed the MS soon after, he spawned a unique form of Susanoo while the others stayed basically the same.
