I disagree that the origin of chakra needed to be explained, as it was there from the start of the series. I never once questioned the origins of chakra when I started the series, as it was just a system in play that brought life to the world, and it was fine that way.
I also disagree that Kaguya was necessary for the story, and Kaguya was only introduced directly as Obito started to activate the Divine Tree. Sacrificing Madara for the incredibly poorly written villain that is Kaguya was a mistake, and also just ruined the character that Madara had been built up to be.
