It was a long read, but enjoyable and well worth the time. While it may have been entertaining and well-posed, I must point out that this Rinnegan business raises the question of continuity. My memory may not serve me so well, so if I'm wrong please correct me and reference the manga chapter(s) and page(s) that apply.
Madara acquired the Rinnegan due to the combination of Senju DNA and his own, correct?
"But people will say that Naruto needs Uchiha DNA/Eyes. Well… all the evidence leads us to believe the Sage gained the Rinnegan AFTER he sealed the Juubi within him. Naruto has gained nearly the entire collection of the Juubi’s collective pieces, minus the 8 Tails (The silhouette showed us the 1-tail, so it may be a retcon and he has the 1 tails chakra as well). Once Naruto gains it, like Derp has hypothesized, Rikudou’s chakra essence will appear in Naruto’s psyche. He will speak with Naruto, we will learn his back story and how to “defeat” the Juubi. When Naruto comes out of it, he will gain the Rinnegan and the ability to use Yin-Yang release to aid in splitting the Juubi (Creation of all things is the highest variant of Yin-Yang release)"
With regard to the bolded portion:
Yes, I am one of those who believe the Rinnegan necessitates complete DNA from the SO6P or somehow awakening it by one's own merits. It is said that the SO6P was capable of manipulating all five forms of chakra release; Naruto can only use wind at the moment (so far as I'm aware). I'm not sure if he's reached the level at which his own merits will awaken this doujutsu. He'd have to reinvent the wheel, so to speak... and for Naruto, that just doesn't seem likely.
With regard to the underlined portion:
You are straight up committing the fallatious and treacherous act of Begging the Question. You state that there is evidence that the Rinnegan was awakened after the SO6P's quarrel with the juubi, and yet you present none of it. Please shed some light on this, because I looked for evidence (although I only spent 15-20 minutes hastily scanning naruto-wiki and relevant manga chapters) and found none. I'd actually love to be wrong on this one, because that would set me at ease with your hypothesis and cause me to insist that it is a valid and note-worthy guess.
With regard to that which follows the underlined portion:
The SO6P stated that there would come a day when all of the tailed beasts would again become one. As it is right now, we are not quite there yet in the story. Sure, the juubi has some of the chakra from both Kurama and Gyuki, but the nine beasts are not yet one, so the "prophecy" of the SO6P has not been completely fulfilled. If the Sage's words shine true, then it would be pointless to split the juubi until that has come to fruition. Otherwise, bringing the other seven tailed beasts together would've been a waste of time -- sort of. Is it possible that splitting up the juubi would serve as a good temporary fix? Yes. Could the "prophecy" still be fulfilled by allowing the nine beasts to reunite after the war and in accordance with Naruto's will? Maybe. The problem is this: what's the damn point of running in circles dodging the words of the SO6P only to fulfill them later? (rhetoric heavily implied)
I did like the hypothesis overall. It just requires some tune-ups and revaluation. 4/5 rating... which is a significantly better rating than other 'theories' *scoffs* that I've read.