First notice that the Tobito theory is not completely unfounded. The similarities are staggering. Tobi and Obi share: Goofy behavior, Hairstyle, approximate age if Obito was alive, Sharingan, right eye only plus Tobi is wearing metal gear on his body which could mean he had his body smashed just like Obito had.
There are still unexplained contradictions in most of the Tobito theories I've heard, but I do not believe that an author who has the ability to avoid such strange coincidences would purposely try to confuse his reader with such circumstancial evidence. So I think it's safe to assume Tobi really has some sort of connection to Obito. The one thing that prevents many from this simple conclusion is Madara. How can Tobi be Obito when every
character knowing more about Tobi calls him Madara? How is it possible that Obito and Madara are the same person - Tobi? This is where theory jumps in.
In order to put the pieces together to a picture I have come to the following theory:
We all saw Tobi stating that his power was "Uchiha Madaras power". He spoke of Madara in 3rd Person. (translators still argue, but the fact that it CAN be translated this way is enough) That was a really odd sentence at the time but it makes sense if you look at it this way. I assume Madara actually did die some time in the past. This allows following chain of events: When Obito was on the verge of death somebody came to his aid and saved his life, this somebody then implanted Obito Madaras eyes granting him Madaras power, maybe even part of Madaras conciousness. However Madara had two eyes why does Obito remain with one? There are multiple explanations.
A) The lame one: Madaras left eye got destroyed B) Slightly less lame one: Obitos left eyehole had already healed and made transplant impossible
C) The contradictory one: we all know the foureyed creature appearing in Itachis Genjutsu. In Madaras case all four eyes were present, but in Itachis case only two were,
indicating that Sasuke has to provide the other two. This would explain why the two can't simply swap eyes, they need to have all four for some reason.
I yet have to figure out where the two original eyes go but i doubt they're pushed back into the skull. The whole idea that Madara removed his own eyes and implanted some others probably without any medical training and certainly without looking at what he was doing and that Itachi is about to attempt the same thing is pretty shaky anyway.
D) From my point of view the most probable: Obitobi has a benefit from keeping his remaining original eye - maybe to hide his identity or whatever. So he keeps Madaras eye behind the mask and uses his normal eye to look around.
(I suggest Tobi is about to reveal his second eye and demonstrate Madaras power. Maybe Kakashi will the realize it's Obito which would settle the case.)
Nevertheless these are explanations why Obito only has one eye, not two. I agree there could be other methods to grant Obito Madaras powers but the eyetransplant seems the obvious assumption.
Now this theory can provide us with some real information. It explaines why Madara chose that particular time to attack Konoha with the Kyuubi. He was dead until Obito
gained his power then set out to catch the Ninetails and then attacked Konoha with it. Everything fits. And by the way this Obitotheory also explaines why Itachi calls Madara a shell of his former self. The shell is Obito.