Okay, guys! I've had a breakthrough. (no, this isn't another troll theory.) I think Tobi might still actually BE Madara. Alright, remember that "Splitting Technique" that Mū used? It actually split his soul into two seperate parts. So, they were actually BOTH the real Mū. Now, we know that Madara fought Mū AND Onoki. So, it's possible, that during the fight, Mū used the splitting technique and Madara copied it with the sharingan. So, Tobi actually IS Madara. The real Madara. Not just a clone. So, right before he gave his eyes to Nagato, he used the Splitting Technique to split himself into two in case something went wrong with the transplant. When one half gave his eyes to Nagato, having a severe power difference to his other half, who is supposed to have the same amount of power, caused his eyes to automatically downgrade back to normal(cuz his eyes couldn't just pop out of his head). After that, something went wrong with the surgery, which started to kill Madara. So, Madara told Tobi to eventually resurrect him. After the death of Madara half #1, Tobi trained to re-awaken his sharingan, since he had no restrictions on his power after Madara's death. However, he could only upgrade it to sharingan. That's why Tobi said that he was just a shell of his former self. He really IS just a shell as he only has half his power. And, when he was talking to Zetsu, he said, "I can't believe Nagato used the Rinne Tensei like that, It was supposed to be for me." Now, why would he need to use Rinne Tensei on himself? Sure, Kabuto said, "I am unsure if the "fake Madara" will act according to plan." But, Kabuto most likely doesn't know who Tobi is. He also could be trying to frame Tobi for Madara not being Rinne Tensei revived, even though it wasn't Tobi's fault anyway. Also, name ANYONE else who has those pronounced under eye creases that Madara and tobi do.
So, there ya have it. hope you enjoyed. And, what did you think of the theory?