Disclaimer:
I made a post regarding danzou a few days ago in order to gain some insight into common danzou theories and people kept telling me that there were hundreds of posts already discussing the matter. Ironically, yet unsurprisingly, when I requested the individuals making these statements to post a link to the hundreds of posts, the most anyone came up with was 4 links to various vaguely related topics, the most recent of which was made in august of last year. So please, keep this in mind before responding with something along the lines "THIS HAS BEEN DISCUSSED 1000'S OF TIMES!!!1" I believe there's been enough development since august to justify a new topic and the issues raised in this topic are significantly more detailed and thorough than anything I've seen that has been posted before. If I am wrong, feel free to link to any post or topic discussing this matter that was made recently.
Foreword
The main reason I want to discuss this is because of a few recent developments involving Danzou, mainly him explicitly stating his desire to become hokage and overthrow tsunade, but there are several others.
Danzou is scheming something, and I strongly suspect Danzou is going to start playing a very significant role in the manga regardless of whether or not anything in this post turns out to be true (which honestly, is highly unlikely). What is undeniable, however, is that danzou is definitely up to something, which is backed by the manga (http://www.onemanga.com/Naruto/424/02/). What he's up to is highly ambiguous and as such, I want propose a possible theory as to some of the extent of danzou's plans.
Unanswered Questions
There are some particularly puzzling questions about Tobi, Madara and Danzou that have yet to be answered. If we assume that Madara = Tobi and answer these questions, we arrive at some troubling conclusions. Feel free to offer responses to any of these question that you feel are more suitable than the ones I've chosen and I'll replace them. These are merely what I've perceived to be common answers.
1) What is the point of the Tobi disguise if it's Madara behind the mask?
There isn't really much point at all.
2) Why would Madara try to infiltrate his own organization?
Again, there really isn't much point. We could come up with a far fetched justification, however, like maybe Madara gets off on pretending to be some low-tier moron in front of his subordinates.
3) Why does Tobi wear a mask?
Again, there really isn't much point. We could come up with a far fetched justification, however, like maybe Madara gets off on pretending to be some low-tier moron in front of his subordinates.
4) Why does Danzou wear a bandage?
The reason for this hasn't been stated and assuming Madara=Tobi doesn't really help in answering this question. Something like this could be as simple as an old injury, however, it conveniently leaves Danzou's right eye concealed. As a result of this ambiguity, nothing can be said on this matter for certain.
5) Why does Kisame not know that Madara is pulling the strings in akatsuki?
Not really sure. We could come up with a far fetched justification, however, like maybe Madara deliberately concealed his involvement and only reveals himself in private meetings for uh...If anyone wants to finish that one off, be my guest cuz I'm really at a loss...
6) How did Tobi not realize that Sasuke failed to capture killerbee if Tobi is actually Madara?
Maybe EMS isn't capable of recognizing a jinchuriki. I guess they are only good at controlling the things...
7) Why would Itachi leave an amaterasu trap that Madara could put out?
Makes no sense unless we come up with a far fetched justification like maybe Madara lost his EMS, or maybe Itachi didn't know EMS could put out Amaterasu.
Summary of some basic facts:
-Danzou has his right eye covered and Tobi's sharingan is in the right eye.
http://www.onemanga.com/Naruto/424/02/ - Picture of Danzou
http://www.onemanga.com/Naruto/364/19/ - Picture of Tobi with sharingan
-Tobi can perform a space/time jutsu that enables him to travel large distances instantly. This kind of ability would be REQUIRED if Danzou was disguised as Tobi in order for there not to be obvious plot holes.
http://www.onemanga.com/Naruto/363/02/ - Tobi about to be blown up
http://www.onemanga.com/Naruto/363/17/ - Unspecified, yet obviously a short amount of time later a shady figure is seen talking to Pain and Konan
http://www.onemanga.com/Naruto/364/18/ - The shady figure is revealed as Tobi
-Tobi only seems to reveal himself as Madara in private 1 on 1 meetings.
http://www.onemanga.com/Naruto/404/01/ - An example
-Kisame is surprised when he learns Madara is the one "pulling the strings."
http://www.onemanga.com/Naruto/404/01/
-Tobi's face has not been revealed to readers.
http://www.onemanga.com/Naruto/ - Obviously I'm not lying, but feel free to double check
-There is a large amount of ambiguity in the manga which could easily lead to an unexpected plot twist.
http://www.onemanga.com/Naruto/ - Again, obviously I'm not lying, but feel free to double check
On to the theory:
I think Danzou has been spying on Akatsuki by disguising himself as Tobi and he has been doing this for a while, while at the same time, trying to gain control over konoha in order to become hokage. Danzou's plan after becoming hokage, I believe will have something to do with the summit of the kage's. All kage's in the same place? Sounds suspicious. I don't dare speculate much further than this as it's already a bit of a stretch.
Note: The summit of the kage's would've been caused by danzou, if danzou=tobi. It would mean that it was danzou who manipulated sasuke into fighting killerbee, the incident which triggered the summit of the kage's.
http://www.onemanga.com/Naruto/417/15/
Only recently has tobi been revealing himself as Madara to members of Akatsuki. In fact, it's almost as if everyone who knows (or thinks, I should say) that Madara is Tobi, has found this out by Tobi "revealing himself" in a private 1 on 1 meeting.
Example:
http://www.onemanga.com/Naruto/404/02/
It seems strange, no? Kisame seems to know Madara quite well yet he was unaware that Madara was "pulling the strings". How is this possible? Perhaps it's because Madara ISN'T pulling the strings. Perhaps it's because Akatsuki is being manipulated by Danzou. Perhaps Danzou is meeting people 1 on 1 so if they ask too many questions, they can be taken care of before anyone else finds out what he's up to.
It sounds to me like Danzou is planning something huge and is using or manipulating Akatsuki by pretending to be Madara. Danzou seems to be heavily exploiting the mystery surrounding Madara.
Something funny:
http://www.onemanga.com/Naruto/424/02/
It seems almost as if Danzou knows how useless Akatsuki is from his experience in the group as Tobi. He would've seen deidara ragesuicide, he would know about hidan and kakuzu messing up, he would've known about sakura and chiyo killing sasori and he quite obviously knows of sasuke's failure to capture killerbee.