a theory a friend of mine and I came up with...
"""If you notice the fight between the Fourth Hokage and Tobi, Tobi has short hair. Then later on when Itachi sought "Madara" out, he had long hair, and then later on to the present he has short hair yet again.
Being confirmed by Madara Uchiha himself that he didn't die after the fight with Hashirama Senju, perhaps Madara lived on and created the "First" Zetsu. Because according to tobi, "Madara Uchiha" gained Hashirama's Chakra/DNA after the fight between the two. Would make since that Madara would have the ability to create a zetsu. But not only did he create a Zetsu, he implanted it with the DNA and memoires of himself and possibly the DNA of Hashirama (if he didn't already have it being a zetsu). And after creating him, they both devised a plan that when Madara Uchiha died, that Tobi would bring him back to life (Some how). Because the real Madara did say that being brought back the way he was (Edo Tensi) wasn't according to plan. And He did make a reference to knowing who Tobi is.
The real Madara being alive at the time when Itachi sought him out would also explain how Madara would know Nagato (based on what Tobi said to Konan, that he gave the rinnegan to Nagato acting as if he was Madara.) and would also explain why Itachi said that he was Madara Uchiha. Because as we all know, Itachi was VERY smart.
Also Tobi collecting all the paths of the sage would also lead me to believe that maybe he didn't have the sharingan to begin with. Maybe Tobi went out collecting sharingans till he found one to his liking. And after the slaying of the uchiha clan he collected some, and later on some how he found obito's body and took that one and became fond of it. Which would explain why his space time jutsu is similar to Kakashi's. And this would also give Kishimoto a reason to make the readers believe that Tobi is Obito, (with the eyes, the mask, and almost similar letters in the names), just so he could turn around and somewhat surprise everyone when he says "It's not Obito, it's ....".
But if this is true; then if you think about it, its kind of a repeat in history. Madara gave his DNA (strength) to Tobi, and his eyes to Nagato. Just like the Sage of Six Paths done when he gave his eyes to the older son, and his strength to the younger son.
Another thing to consider about Tobi being a Zetsu and looking human-like. At the fight with Kisame and Killer B, White Zetsu made himself look exactly like Kisame, and had the exact same chakra.
Also when Tobi mentioned to Pain that he was Madara Uchiha it kinda seemed as though He believed it, which could be a reason as to why Tobi assumed "true" leadership of the Akatsuki, and would be another reason to show that Nagato really does know Madara Uchiha.'''