Well.. now i think that Kishi is making fun of us. Tobi is not Madara and Pain is not Nagato.
You can think i'm crazzy but you'll see.
I think Pain is the real boss of Akatsuki that tricked even Tobi. Tobi wants to become the new Uchiha Madara but he needs Sasuke's Eternal Mangekyo Sharingan. That's why he wants Sasuke to use Itachi's eyes and create the EMS. As we know , we never saw Tobi using Mangekyo S. or EMS so he must take Sasuke's eyes for that.
If Tobi is Danzo than that explains this: Danzo sent Sai after Sasuke to test Sasuke's compacity and make sure Sasuke's Sharigan progression continued. Remember Tobi also allowed Dedaria to fight Sasuke to the death by himself , only for the same reason.
So Danzo needs Sasuke's EMS to become the new Uchiha Madara ( Master of the Sharingan )
And for Pain , i think he controls Akatsuki and Nagato. Who is Pain ? hmmm maybe Rikudoo senin ... or Konohamaru's father or a new character ..
One thing is for sure , Kishi is trying to look foolish but he knows what he's dooing