CrustaceaN

Let me try to be like Kishi for a sec...

Nagato is now a Senju, yet he has Red Hair and is an Uzumaki.
Since Uzumaki are automagically Senju according to Kishi's disinterest in his own series, Naruto is now a Senju.

Naruto will receive the Sharingan from Obito/Kakashi(it will happen) and Shisui's Sharingan from somewhere, anywhere depending how Kishi feels. Shisui will end up being a sibling of Obito somehow, someway(don't ask, it's manga fact). Naruto will combine both Shisui's MS and Obito's MS to create a fucking OP EMS. Kotoamatsukami and Kamui.
Blah Blah Blah... since Naruto is Senju and will have Kotoamatsukami and Kamui/EMS he will awaken the Rinnegan.

Since he knows the names of the Biju as well, he will become the Sage... yet he knows Senjutsu.
Naruto will combine Yin/Yang and Natural Energy to do something rainbow-like, because that's the theme for part 2, and everyone will eat cake from the North to the South.
Solved.

Kishi, take a break... I got this.

I feel violated for that attempt.