So i saw this theory on a thread and suddenly everything became clear to me. Please follow me on this one and read completely.
{[ Originally Posted by dgreene196
Maybe Tobi took the eyes after Madara's death and implanted them into Nagato.
I think Nagato was used as a useful, convenient tool. It's been fairly solidly established that, for an Uchiha, it takes little chakra to maintain the sharingan. But that's not true for MS for the Uchiha or regular sharingan for non-Uchiha (why both Danzo and Kakashi keep their eyes covered when not in use). Those variations of the sharingan require a great deal more chakra. For Uchiha, the EMS enables more freedom with the MS techniques. Imagine how much chakra the Rinnegan requires, especially for someone who wasn't born with exceptional chakra (it'd be kind of like when Tenten used the Bashosen). Nagato, as an Uzumaki, reportedly had unusually strong chakra, which might have been necessary to control/survive use of the Rinnegan. And, possibly, like non-Uchiha who have sharingan implanted into them, Nagato wasn't able to "deactivate" the Rinnegan into EMS, etc. ]}
still this explains everything after mandara was in possession of the rinnengan.
According to this theory, it means that nagato didn't awaken the rinnengan meaning the senju(relatives of uzumaki thereby sharing the same dna) can't awaken rinnengan because they lack the eyes but however they have the body to handle the rinnengan, on the other hand it also means the uchiha has the ability awaken rinnengan but they don't have the body to handle the rinnengan so can't awaken it, so madara truthfully did not die but rather as he said he acquired the first's dna in their battle and has now completed the two requirements to handle the rinnengan, which is how he managed to awaken rinnengan.
Now this perfectly explains madara, but now what is tobi?
My only theory on tobi is that he is a being created my madara that comprises of a white zetsu's body and Obito's head (mandara decapitated obito's dead body)
Proof: The body:
http://www.mangafox.com/manga/naruto/v52/c486/5.html look at what madara uses to replace the arm he lost in his battle with danzou's boys, it looks exactly like zetsu.
The head: look at the same link, we have never seen the left side of madara's face but if you look closely, it appears to be a lot smoother than the right side, and we've always been shown the right side which is wrinkled, and the right side it the side that got hit by by the rocks in obito's face and that's the side which also possesses his other sharingan that has been shown to possess the same space time ninjutsu ability as kakashi's ms which is obito's other eye. Explains why tobi says "that won't work" on him doesn't it?
http://www.mangafox.com/manga/naruto/v52/c487/4.html he possesses the same technique it's like trying to hurt water by pouring water on it, won't work right? same thing.
Further explanation: since the head was transplanted, tobi lacks the ability to deactivate the sharingan that's why he's shown with it activated all the time just like danzou and kakashi, on the other hand it doesn't put much strain on his body because white zetsu is made out of senju's dna (remember this allowed danzou to use so many sharingans and even prolong the lenth of izanagi) and this is also the reason why tobi is able to use izanagi however still at the expence of a sharingan on his left side which he transplanted from his numerous sharingan collections. And notice even after 25% of the mask was broken kishi still managed to hide the left side of his face in complete shadow.
http://www.mangafox.com/manga/naruto/v54/c510/10.html
To tie everything together, mandara fought hashimaru senju, lost and acquired his dna, awakened the rinnengan, created tobi, and started the experiments for the creations of the white zetsu army, died later either due to the injuries he received from his battle with the first or old age and of course after giving orders to tobi to transplant the rinnengan to nagato an uzumaki(relative of senju) who has the body to handle the rinnengan, so when nagato get's older and masters the rinnengan he could revive him using gedo rinne tensei no jutsu. Which explains when he says, so nagato finally grew up, and after realizing he was awaken with edo tensei he says it's not according to plan.
And that's the complete theory please remind me of any facts i left out, or didn't explain, comment, and share your thoughts.
