As stated, the only thing that bugs this whole theory is Madara controlling the Mizukage. Now...
1. We know that Obito took on Madara's name after Madara died. Shortly after we see him talk to Yahiko, Nagato and Konan about forming Akatsuki. Now he might have had that idea a long time ago but it was Yahiko and Nagato that created the organisation. Fact number 1.
2. When Madara/obito reveals himself in front of Kisame, he asks him to join his plan and to join Akatsuki. Fact 2.
Here is where it gets interesting.
If Madara/obito revealed himself in front of Kisame BEFORE the conversation with Yahiko/Nagato, then we can safely assume that it was indeed Madara who was controlling the Mizukage. In that case, the moment Tobi dropped his mask, Kisame should have noticed that it wasn't Madara behind the mask but Obito - a rather unfamiliar character to him.
If Madara/obito revealed himself in front of Kisame AFTER the conversation with Yahiko/Nagato, then we can safely assume that it was actually Obito who spoke to Kisame and pretended to be Madara. In that case Kisame would have no idea how Madara looked and would take his words for it. He would also react the way he did after Tobi dropped his mask as he would have seen Obito's familiar face.
Obito/Tobi was never revealed to have any particular Genjutsu skills so the idea he controlled the Mizukage for that long vexes me greatly. But it could be that it wasn't relevant to the story. In any case this is the ONLY moment in the manga that can be disputed and wer still have no solid proof or accuracy when it comes to timelines in NV.