The More I think about it, the more convinced I am of some of my ideas above.
1) Uchiha Madara hatched his Moon's Eye plan WAY BACK in Hashirama's day.
2) He needed the Rinnegan, and for that he needed Hashirama Senju's Genes
3) He decided to challenge Hashirama in battle, and collect some DNA from their mutual blood letting
4) He Knew that he could die, but he had a back-up plan for that
5) Madara creates a backu up plan, using a Zetsu Clone that will carry out his plan if he should die in the battle
6) The Zetsu clone has Madara's Chakra and some random Uchiha Eyes.
7) The Plan was for the Zetsu Clone of Madara to Infuse itself with Hashirama's DNA, and using Madara's Chakra and spiritual energy, it was supposed to evolve a Rinnegan, with the Rinnegan the clone was supposed to revive Madara (only if he got killed in the fight, else Madara would do all this himself.
8) The fight happened, Madara lost, the Zetsu Clone Madara got Hashirama's DNA, everything seemed to be going according to plan.....except.
9) Something went wrong, The Zetsu Clone COULD NOT evolve a Rinegan, and Madara stays Dead. The senju DNA from Hashirama was not enugh, the Rinnegan Process probably required a living being with the strong Chakra of a living powerfull Senju or better still an UZUMAKI, and that person must be under Duress to force the evolution to happen. This just like the Mangekyou Sharingan requires a strong emotional event for it to evolve.
10) The zetsu Clone began to act independently, but having been made from Uchiha Madara's spiritual energies and Chakra, it went ahead and plotted to complete Madara's original plan.
So Tobi is Madara in every way that counts, his knowledge, his desires, his will, but he is not the original Madara.
SO where's the original Madra? Answer is, he's dead and Kabuto has the body. He may even have revived it but kept it inert. That's as far as I've thought it through. Guess we'll find out how it goes soon enough.

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