As you all know, Chapter #560 came out a while ago, and many people said that it explained nothing and just showed off Uchiha Madara's god-mode abilities and the Rinnegan. The previous chapter, #559 revealed that Uchiha Madara DIED at about the time he fought Hashirama, as his resurrection shows no true signs of age.

My theory behind the mask:

I think it'd be best to start from the very beginning before Konoha was founded, when Madara and Izuna had the eye exchange. In this part, Tobi explains to Sasuke that he takes HIS BROTHER'S eyes. At no point does he say he takes Izuna's eyes, and this is probably the strongest argument for Izuna being Tobi. You can also say that his fear of the real Madara is another strong factor, but I say that Tobi not explicitly mentioning taking Izuna's eyes is the strongest argument.

For now, we'll say Madara took Izuna's eyes, as it simply flows with the rest of the story more smoothly. Now, Madara obtains EMS from the eye exchange, killing Izuna in the process. Fast-forward to Madara's fight with Hashirama at the Valley of the End. Now, keep in mind Madara's abilities:

Madara has:
Kyuubi
EMS
Just insane abilities in general

Hashirama has:
Mokuton
1st Hokage Hax
Bjuu control

I believe that the battle went like this: Hashirama extracts the Kyuubi with his control, and seals it (as he IS a distant relative of the Uzumaki) into a scroll or something. However, being Madara, he still lives and continues to fight, although the loss of the 9-tails takes it's toll. Madara then awakens the Rinnegan at The VotE, and manages to salvage some of Hashirama's cells (probably using some function of the Rinnegan). Hashirama leaves Madara to die, and returns to found Konoha.

Madara, still alive, although gravely wounded and short on time, uses the Senju cells and his own cells as a basis for the creation of Zetsu- a genetic combination carrying Hashirama's cells and Madara's cells. Madara then dies, but sends Zetsu on the mission so that he can one day become complete with the 10-tails and be 100% revived, unlike his state through Edo Tensei. He orders Zetsu to take his Rinnegan eyes after his death (explaining why he still has the Rinnegan) and find a worthy host. Zetsu searches for years until, during the 2nd Shinobi World War, he finds Nagato and his parents. Every single "Konoha" shinobi that attacked Amegakure was a white Zetsu clone (I believe), including the two shinobi that killed Nagato's parents. Zetsu finds Nagato alone, and decides that he shall be the new host, and knocks him unconscious and then transfers the eyes into Nagato. Nagato awakens to find the two shinobi that killed his parents dead, and believes that he killed them. In actuality, it's just a setup by Zetsu.

Years later, the 3rd Shinobi World War breaks out, and Zetsu is still trying to find a host body for Madara to temporarily use. He needs an Uchiha so that he can achieve Izanagi- something that was out of his reach, but with Zetsu's cells, could be accomplished. Zetsu finds Obito crushed under the rocks, and using clones or w/e removes the rocks and finds that he still has a sharingan- his right sharingan is still intact. Zetsu immediately responds to this by using Obito as the temporary body for Madara, and restores him using his own cells and Madara's cells, giving the "dead" Obito new life, being revived by Zetsu. Now "Tobi" takes on the mind of Madara- all his memories, everything except his physical body- and Madara is now amongst the living. Since Zetsu had Madara's cells, he now knows everything that Zetsu had done, including whom he gave the Rinnegan to. Using Madara's knowledge of MS, and Obito's sharingan (which has similar effects to Kamui) he tracks down Nagato, Yahiko, and Konan, and convinces Yahiko in one way or another to create Akatsuki.

Keep in mind that Tobi or Obito or Madara (whomever you want to call him) only has 1 sharingan now, his RIGHT sharingan, and he will only have one sharingan UNTIL the UCHIHA MASSACRE, when he steals a random sharingan eye to use for Izanagi. Tobi then fades away into the background as he watches Akatsuki destroy and capture the Bjuu so he can create the Juubi.

Since Tobi is Madara, it explains why Madara knows Nagato's name, and also answers any doubts addressed towards the Tobi IS NOT Obito campaign. "Obito wasn't old enough to have fought Minato". This is a false statement as Kakashi is shown to be about 16, and Obito was about 2 years older than Kakashi, making him eligible to attack the Leaf Village. Also, since Madara was still alive after Madara defeated him, he had seen where Hashirama had sealed the Kyuubi, and followed it's pathway down to Kushina. As a former host of the Kyuubi, it would make sense how he was able to summon it through a blood contract. The Kyuubi (despite probably not liking being controlled) probably wouldn't have resisted Madara as he would have others- he loved Madara's strong hatred, and embodied it. Since Madara didn't have the large chakra and physical ability that his natural body had, he wasn't able to maintain control of the Kyuubi as much as he wanted to.

"Obito's DEAD, and he can therefore not be Tobi." Even if he is dead, Zetsu could take care of that. Chances are, however, that he never DID die for good, as he's not among the resurrected in the Edo Tensei Army, and is rather just a body taken over by Zetsu/Madara, although he still lives. In episode 215, we see Tobi's right arm being white (like Zetsu) while his left is normal.... coincidence? I think not.

I also believe that Zetsu used to be entirely white, but since he had to use his right half to heal Obito's body for Madara, only his left half is now white, while the other is black (don't know how the black half was made though).

Also, Tobi [Madara] could've feared his own body because he planned on reviving it himself so that he could become "100% complete".

If there's a point I missed, or you want to comment or add new ideas, just post below.