In my opinion Tobi is Danzo, yes you guys will probably first think WTF.
However think about the naruto as a whole.
Danzo = Leader or "Root"(a high powered ANBU section)
Itachi = Akatsuki member(ex-ANBU commander)
Sasuke = only survivor of Uchiha massacre(3 members alive total)
Tobi = Akatasuki Leader(age ?)
Root = ANBU section that trains children from a young age(info from wikipedia).
From those above, It seems Itachi was trained under Root as he was an amazing child who finished chuunin exam at a very early age and enter ANBU at an early age. From Tobi's recent statements it seems he is trying to achieve Uchiha Madara's powers( "The Sharigan's True Power... My Power.. Uchiha Madara's Power...). Therefore, he means that there is some sort of secret behind the Uchihas other than mangekyo. Itachi killed everyone in the Uchiha except Sasuke for reason unknown, though he said to test his power. Now in the latest chapter Uchiha says meet me at Uchiha hideout. Why There? Although it makes a good setting for a final Uchiha fight, I doubt Itachi would ask Sasuke to fight there without a good reason. My hypothesis concluded from this that Danzo is or has Uchiha powers and commanded Itachi to kill all the other Uchiha to eliminate competition for Madara's Power. Why didnt he kill Itachi then? Well because Itachi achieved the Mangekyo Sharigan and Kakashi is proof that there is more than 1 evolved form of the sharigan. It is likely that when one reaches this new sharigan that is the final form; Madara's Sharigan seems to be far superior to Itachi's and Kakashi's. If so, Itachi was no longer a threat to Tobi and was more of a tool. Since if Itachi killed Uchiha instead of Tobi than no one would be suspicious of Tobi. Furthermore, isn't it kind of strange that Danzo commanded Sai to kill Sasuke? If he really wanted to kill Orochimaru, he would have sent in more ANBUs after his hideout, which would get him recognized better as the one who silenced Orochimaru. But since Sasuke has become a Missing-nin and is no longer protected by Konoha (since every1's eyes were on him as the last uchiha which means a large protection from Konoha). Therefore, he was more vulnerable to kill or considered to be until Pein comments about how Sasuke has become a threat now. But since, Pein isn't the true leader, tobi must have commanded Pein to make sasuke in to a threat. Also its strange that Danzo has the right portion of his eye covered up by a bandage, while Tobi has only his right eye shown, which would be an easy and ultimate disguise. Now Danzo is definetly powerful because he was rivaled with Sarutobi for 3rd Hokage, but he is very war hungry. Tobi seems also war angry because Pein said the plan for Akatsuki is for a war against all countries, but taking over a country with just 10 members is hard even with 10 S ranks, which has been reduced to 6(NOTE: although Sasori claimed he took over a country). We also know that Konoha is Biggest power house in the nations because of the ANBUs, Kyuubi, and Hokage. But 5th is no where strong as 4th and Kyuubi is suppressed in Naruto and if ANBU is under Danzo's control then Konoha would be very frail. However in order to wage war against countries Akatsuki has to have a country of its own. The hidden village of rain is about to be taken over by Tobi and Tobi is Danzo. Then taking Konoha over would be very simple for them and taking out the strogest country first is like finishing the war. Also, I really doubt they will bring out a random new character to be Tobi and I think Obito is not Tobi cuz the right half of his body which means no right eye. I also doubt 4th is Tobi cause his name was released and it doesnt contain Uchiha and he DIED after sealing 9 tails and Orochimaru's jutsu is proof that 4th is dead(the zombie hokage summoning jutsu). Also ROOTs motto is no emotions, but Danzo the leader would probably have mastered emotions, which results in Tobi's happy mode. Also I think collecting all the tailed beasts is a requirement for Madara's sharigan as in the chakra from them.
Please comment and also post flaws in my theories if there are any.