My theory: Tobi = (part of) Madara with Obito's body, fixed with the help of Zetsu.
Here is how it goes. In the Battle with Hashirama Madara almost died, somehow the Rinnegan saved him. But he was weak, in no condition to fight anymore. So he goes away, searching for away to return. In that times with the cells of Hashirama he creates Zetsu, or improves him...
Since Madara is to weak to use the Rinnegan he decides to give them away to young Nagato (Tobi explicitly states this to Nagato's help Konan), who is being trained by the legendary Sannin Jirayaia. Madara know this is the way to develop the Rinnegan, so that in time he can be revived by it. But before he does so he needs other eyes. So together with Zetsu (he that is one with the land) finds Obito. A weak almost dead Uchiha, one he can defeat even in his (Madara's) weak state. Now here comes to tricky part I think that somehow he transferred part of his soul / chakra / skills into the body of Obito, and likewise gaining his eye ability. The broken body than got fixed by Zetsu. How the transfer went is vague but this is very likely (I mean Oro can do it), why: for two reason In the beginning Tobi only has one eye, ofc because Kakashi has the other. Also, in the recent episode where Tobi got hit, on the RIGHT side, the side that was crushed by the ROCKS (remember OBITO) you see some white skin. Ofc that is the side ZETSU fixed.
Furthermore: the combination of Zetsu and Madara makes it possible that he fights Minato and knows all these things about everyone, cause in the end he is Madara. But as Itachi has put it: A shell of his former self!
Dont you think it makes sense, in the end I will it seems quite obvious even! One last thing, Edo Madara talks about our little plan!