Give Naruto more interaction with the Biju prior to cramming it all in so quickly and give them some actual world building. Too much of the story was dedicated to the convoluted Senju/Uchiha bullshit dichotomy and it didn't tie in well Kaguya and the Otsutsuki, chakra origins, the Juubi, etc.
Shippuden should've been written with Naruto and Sasuke going into divergent paths with Naruto learning the ways of the Sage at Mt. Myoboku as well as rescuing, training, and getting to know the Biju and jinchuriki and Sasuke taking Itachi's eyes and power, developing the Curse Mark to a third stage, and learning the truth of the Uchiha. Then they could have clashed fists and philosophy at VoTE 2 and the ending would remain largely the same.