Orochimaru's Test Subject:
I don't think Nawaki died like it was stated. I think Orochimaru faked Nawaki's death to experiment on him.
It also has been shown that Orochimaru will use corpses to throw people off his trail.
Why did he do this? Well it was hinted that Orochimaru was Nawaki's master. He probably saw signs that Nawaki inherited the 1st Hokage's abilities & it has been shown that Orochimaru was obsessed with collecting powerful abilities.
Now he used Nawaki's body (Senju cells) to create an early version of White Zetsu. After these experiments were done Nawaki was changed forever, he eventually became Tobi. He began to hate his grandfather more & more everyday. Although he never stopped admiring him. This would explain his feelings toward the first.
Eventually Orochimaru twisted his mind & made him into the person that he is now. He became a tool for Orochimaru to use. His "Childish Tobi" personality is a split personality caused by him being taken at a young age.
Madara had a partner
I believe the "he" that Madara was talking about was Orochimaru. Who else could he think revived him as an Edo. Orochimaru being his accomplice would also explain how Kabuto got Madara's DNA. The person Kabuto said he was supporting was probably Orochimaru as well.
Tobi in the Akatsuki:
I believe Madara & Orochimaru were the founders of the a group that would eventually merge with Akatsuki. Tobi took Madara's spot after he died. When Orochimaru left the Akatsuki he left Tobi in charge behind the scenes, while constantly keeping tabs on him. Orochimaru planned to take Sauske's body & use it for Madara's original plan. Tobi took on the role of Madara permanently only after Orochimaru died. Tobi changed their plans after he took over.
More experiments on Nawaki resulting in the "The Rinnegan Scroll":
When Madara used his EMS Eyes on the Tablet Naka Shrine, it explained that "The body of the Sage" could be used to unlock true power.
Madara needed someone with Orochimaru's skills to gain power & had heard whispers of the Legendary Sannin's experiments with the 1st's cells. The result of the experiments done on Nawaki had two effects. The first result of these being the creation of the Rinnegan Scroll & The second is the removal of Nawaki's birthright. By this point Nawaki's body has been changed past the point of no return, everything that made him Senju was taken from him. This event is what made him "incomplete" & "A shell of his former self". The scroll that Orochimaru created is also the scroll that Suigetsu & Juugo found.
Tobi's new "Moon's Eye Plan"
Tobi grew up during the second ninja war. He saw the horrors of war for himself at a young age. He himself has stated what that does to a child
What if "the child who grew up in war" that Tobi was talking about was actually himself. During the war that's when he started thinking about his perfect world, A world without war. This thought would grow in his mind & eventually become the "Moon's eye plan".
His Age Fits The Timeline:
Orochimaru had Senju DNA at least 10 years before Naruto was born. This is based off the fact that Yamato was said to be implanted with the cells shortly after his birth. Yamato is 10-11 years older than Naruto.
Nagato died when he was about 36 years old. So when Yamato was born Nagato would have been 8 years old. Which was about the time his parents died & was first seen with the Rinnegan. This would place Orochimaru's experiments during the second ninja war. That's the war that Nawaki "died" in.
Nawaki would be around 40 years old now & 23 years old during the Nine-Tail's attack. His age is one of the few who fits Tobi's projected age.
Why Kabuto Didn't know about Orochimaru's previous experiments:
The simple explanation is that Orochimaru was teaching Kabuto. What would be a better test for him? He wanted to see if Kabuto would come up with the same results. If Kabuto were to come up with different results. Then he would have discovered another way to unlock the Rinnegan. Win/ win for Orochimaru.
I Found some evidence supporting my theory...
From a Kishimoto interview in 2008:
"Three new members will join the Akatsuki. They will be stronger than Deidara, Hidan, and Kakuzu. One of them is the brother/sister of the Hokage..." ~ From a Kishimoto interview in 2008.
