The Tobi = Obito= Danzo theory still holds water in my book. It answers too many questions.
Two Assumptions concerning this theory:
I'm going to assume that Madera has survived so long because he has a sharigan ability to somehow transfer/take over the body of another sharigan user.
And I believe that Madera has a eye technique that allows him to manipulate time.
This would answer a lot of questions such as:
How did Madera survive the fight with the first hokage? It wasn't him, it was his brother. When he "took his eyes" he really changed bodies with him and lived on
How is Madera still alive? He's surviving somehow, and I don't see how else an eye technique can make you immortal
Why did Itachi obliterate the entire clan? To prevent Madera from body hopping and living on
Why does Madera say after Sasuke beats Itachi "we need to get Itachi's corpse" (396/07) He needs it for some sort of potential transfer jutsu
Why does Madera keep Sasuke alive? Because he plans to take him over OR he knows Sasuke's goal is to re-establish the clan which would allow him to live on
Why is Itachi coughing blood going into the Sasuke fight? He somehow injured himself resisting Madera's transfer jutsu
Why does Madera say "I know everything there is to know about Itachi" (397/16) Because he is Danzo, who is head of ANBU which Itachi was once a part of
It makes more sense to me to think that Itachi decided on his own he had to stop Madera at all costs, than the Hokage told him to butcher his whole clan. It makes more sense that the Hokage doesn't know about Madera and doesn't understand Itachi's motive, and instead labels him a rogue ninja.
Now the Obito theory:
The only reasons I want to believe this is because it explains how Madera is alive, and the whole 1-eye aspect of the mask. The one eye isn't just a coincidence, it has to have a reason. Either Obito actually survived when they thought he died, OR it has something to do with the Space/time ninjutsu aspect of the sharingan. This would basically mean Madera has some ability to control time and can manipulate a corpse back to life and then take it over.
Now I know this leaves a ton of things up in the air, and doesn't answer every potential question, but if Madera can manipulate time in some fashion it makes about as much sense as possible to tie all these things together. It explains how Madera, after getting hit with Amaretsu from Sasuke, is able to go to the shadows and come back unscathed.
The theory does have holes. Such as, if he can manipulate time, why does Itachi kill the clan off to prevent Madera if he can just go back in time and take over a dead corpse? Only time will tell I suppose....