Wouldn't that make Madara a huge waste of time? One uchiha becomes juubi jin, kicks all the ass, looses, then gets taken over by black zetsu, who then revives another uchiha who kicks all the ass, becomes juubi jin, looses and then gets taken over by black zetsu. Why not just have Kaguya revived through Obito?
Well...Madara still gets to cast IT so he's not a complete waste of time. That's practically what happened in the manga too. Obito could've been the one to cast IT and then BZ does his thing but nope.
It would also be good in my opinion for Madara to experience the same punishment Obito experienced. Thinking he was above everyone else when in reality, he was just a pawn as well. It's like Madara being in Obito's shoes being done the same thing he did to him.
Also the Naruto and Sasuke that beat Madara in my scenario is the two halves of Hagoromo's power (Madara believing to have reached Hagoromo's level only to be defeated by his "full power" non-Jinmode.
Then when Kaguya comes along and beats them, Hamura gives his power to them as well putting them at Hagoromo and Hamura's level. (Obito, Madara, and the Hokages dying while Nardo and Sauce acquire Hamura's power)
This time, Naruto and Sasuke are able to defeat Kaguya the way Hagoromo and Hamura were able to defeat her. I wouldn't mind a few flash backs of the Kaguya vs Hagoromo and Hamura fight during this fight either.