Nice theory, I rep u for putting text on it, though I have always thought it would be like that, however, I believe that Madara started by creating a black zetsu from his fight with Hashirama. This guy then created the white "bacteria", and yet this black zetsu had some sort of memory left from Madara, but just what he needed to continue Madaras plan, after Madara died, by instructing Zetsu to give rinnengan to nagato. Later black zetsu became so powerful that he started to turn a bit from Madaras first plan. He found ways to make himself stronger, for instance he collected new eyes that he could use to make him stronger, and finally he found the perfect vessel, Obitos body.
Obito was dead but only half his body was destroyed. Black Zetsu then split up his chakra in 2 half beings, and he fused one of them with the "less" smarter white bacteria, and he kept all his sencory / emerge with nature - ability inside this part - meaning most of the ability from Hashirama. Since he didn't really have any uchiha blood, this now actually made it possible for him to use the Rinnengan (I have another theory on how Nagato could use them, but wont talk about that now, since it's obvious anyway).
However, at this point Nagato was already too powerful, so he just kept using him, in fact it was his "luck" that he was defeated in the end, and that he didn't have to revive Madara, cause now he could do it all himself. So now he saw the perfect possebility to declare war and become the greatest "hero" (in his own mind) in the history, finally making him able to regain a "personality" so he wouldn't just be some "mutation" created by Madara. Which is also why he chosed to go off from Madaras plan (as Kabuto said to Madara).
good work bro 
