First off this is a discussion about Tobi and his identity if you are not up to date or have no interest in reading another one you should move on.
My theory is based on the way Kishimoto writes and the actual story. Everyone knows about Kishimoto's constant twist after twist (M. Night Shamolon should call him Kishimoto sensei). He is very good about leading you on a wild journey of lies and deceit only to find out the truth was right there at your first step. Itachi for example, good brother turns into bad brother who is in all reality a good brother. I personally think Kishimoto is just a fan of the HEAD-F**K no JUTSU.
Now for my prediction I believe it is the eldest son of the Rikudo Sage: the Uchiha clan ancestor. http://naruto.wikia.com/wiki/Uchiha_Clan_Ancestor
I do not really know if I am the first one putting this suggestion out there or if I am the millionth because I am new to this posting thing, however I do have reasons to back my claim.
- As I said I am going off of Kishimoto's writing style. He likes to give the answer arbitrarily. So no one notices until it is revealed. Take the first time he revealed Tobi as Madara. He was mentioned by the Kyubi once and Sasuke did not know who he was. Then when Tobi was revealed as Madara most people, not the Obito nuts lol, just accepted it because it made sense. Tobi himself mentioned the Uchiha clan ancestor to tell a story but past that no one would even consider him because he is so far out of scope of the story just like Madara was.
- Tobi has so much knowledge of the Mangekyo Sharingan and it's abilities and yet we have not seen his at all. My theory (and I will concede that this is merely conjecture) is that his eyes over time simply devolved. The Uchiha Clan Ancestor (UCA) has a swirl pattern unlike his father who has the Rinnegan which is a Ripple Pattern. Over time his eyes devolved "gaining" all the Mangekyo Sharigan's abilities as they did. Finally they devolved into the regular sharingan which is where they stayed. This conjecture is given some credence due to Madara having the Rinnegan.
- Tobi also has very intimate knowledge of the past concering the Rikudo Sage. The sage is a myth to most but somehow Tobi knows everything about him and his family. Which gives a lot of credit to him being UCA because how else would he know?
- Tobi's purpose for collecting the tailed beasts is for the Moon's Eye Plan. He said that he wanted them so he could become complete. I believe what he means by complete is that he will regain the powers he had before or more likely the power of the Rikudo Sage, his father.
- Another classic move from Kishimoto is the word bait and switch. When Tobi told Konan he "gave" Nagato his eyes it was confusing to me. If Tobi literally gave them to him how did he get them? Took them from the Rikudo sage eyes kept them preserved for decades upon decades until he was ready to make his move then implant them in a kid he hardly knows without him remembering any of it (because if he had he would have told Konan about it) and then hopes beyond hope he turns out the way he needs him to for his plan? Possible, but extremely unlikely. However he could mean that Nagato is his descendant. Tobi tells us Nagato is from the Uzumaki clan which means one parent is technically Senju, while the other we do not know. In the anime the mother is most likely Uzumaki because of her red hair but what if his father was a descendant of some lesser branch of the Uchiha clan (he has jet black hair). Then Nagato was not only Senju but also Uchiha just like the Rikudo sage. Which is why he could awaken the Rinnegan. Thus Tobi/UCA gave Nagato his eyes figuritively.
That is all I have for my reasons. I feel it is fairly acceptable but if you disagree please let me know so I can either give you a better explanation or I can start to try and figure out another canidate for who Tobi is.
Before I go however I will address one problem you may have with my theory how old Tobi would have to be. Yes I understand he would have to be freaking ancient for this all to work. Do not forget however everyone simply accepted Tobi was Madara even though he would have had to be at least 110 years old for it to make sense. So while I am trusting that you take a bit of a leap of faith with the age thing it is not nearly as steep as it would seem.
I hope you enjoyed my theory and I can not wait to read your replies!