Yeah, I'm going to very much assume that Danzou is not Tobi. I don't think they have some deal going on either. I think Tobi has his own plans, and was the person that controlled the 4th Mizukage. Kisame knew of this the entire time, which is why when a new Mizukage was elected, he became a missing-nin and got the hell out of there.
The question that should be asked is: What is Danzou's connection to Orochimaru? Danzou has definitely been involved with Orochimaru, and I think that might be a major piece of the puzzle.
As for Uchiha Shisui. He had his own techniques using his Sharnigan and I think it is in no way connected to Tobi.
It's still a mystery as to why Uchiha Madara where's a mask that has only one eye hole. I don't know what's up with his other eye, or if he still even has one. There are just so many people with one eye Sharingans, from Madara, Kakashi, Obito, Shisui, to Danzou. It becomes difficult to gauge who is who sometimes