I think you underestimate Danzou too much. Danzou surely was the one pulling the strings. That is his speciality, and he has been doing for more than 50 years... It doesn't matter, if he is near them in terms of strength, since this subject has nothing to do with strength. It has everything to do with influence, however, and Danzou has that much more than any of his pawns. Besides, I can create a 100 situations where Danzou solely defeats either of them in a 1 vs 1.. Itachi didn't have MS, when Shisui still lived, and gaining MS wouldn't give him Susanoo, amaterasu, etc. instantly. We saw how Sasuke didn't get it. And we can easily assume ,he didn't need it for the massacre, as he had Obito's help, and the Uchiha "leader", his father, did not resist.
Also you are wrong on the point, that Itachi had Shisui's eye. Yeah he had it, but it needed 10 years before it would work, so it was quite useless as the time.
Also we don't know anything about how Danzou took Shisui's eye. However, some smaller calculations will show, that the eye he gave to Itachi was still inactive at the time, so he must have used his other eye on the Uchiha meeting, so it would also be inactive, so he had no MS tech's to fight Danzou with. And beside of that, we know nothing of his abilities, so nothing can be assumed on this fight, except the bold stated in the manga.
I don't think Obito had anything to do with it. It's possible he knew about the situation and all, but no way he knew about the Konoha top's doing. Just see how Danzou had no idea, who he was, even believing it was Madara. So I doubt Danzou and Obito ever met - well that is since the Uchiha massacre of course (as stated in the manga).