I read your previous thread about what unlocking MS and EMS allows one to read before I read this (just to get a sense of continuity) and, wow, it is insane how similar we see this story progressing. I wish I had gotten to this thread earlier when you wrote it, but honestly it was just nice to see such a sublime collection of ideas.
If you happen upon my post and want to respond, here is my rebuttal...
First, I agree with you here...
1. The Sharingan's abilities stem from the Juubi
2. The Bijuu were created to learn about humanity. But remember, their collective consiousness have become one now, and this wasn't by accident, the Sage planned it that way. He even told them they would become one again. That is why the Kyuubi and Hachibi have to be absorbed as well, I think in the Kyuubi's case, it may even be willingly.
3. Pretty much the overall message of the Sage and his understanding of balance.
So here is where I disagree.
1. The Juubi and the Sage
We both believe that the Bijuu were created to learn how to live with mankind, however, we must accept the fact that this wasn't a permanent solution, for even the Sage himself said that they could not remain apart forever. With this in mind, I believe that the nature of the Juubi can't be as primordial as you make it sound. In your thread, it seems that the Sage just happened upon the Juubi without understanding much about it. He, of course, saw it's amazing feats and felt its energy in the earth, but I think he understood even more about it than you seem to have written in your thread. If the altercation went as you explained there would be no reason to piece the Juubi back together, something he even left instructions on how to do. So I think that the Juubi was only protecting itself (and by extention nature) and the Sage understood this. He thought Ninshu was the answer (remember he thought it would bring peace) and thought mankind merely needed more time to understand it.
2. The Sage's Understanding of chakra before he encountered the Juubi.
This is purely speculation for it is something we can't really know until we are outright told one thing or the other. But, I have to disagree with your explanation of how the Sage came to understand chakra and here's why.... What we know now, is that the Sage possesed several tools and they all seem to be related to Fuinjutsu (and we don't even know what kind of power his staff held). But as of now, it would seem that his power revolved around sealing more-so than Ninjutsu (Ninshu). You made it seem like his seals were sort of an after-thought after he had exhausted all of his Ninshu techniques (the combining of elements and so forth). And there is a reason I think he wasn't able to control the elements like you've stated and that is because of the Nature of the Rinnengan and its power. I can't tell if you agree with the fact that the Rinnengan comes from the Juubi, but if you do then think about it... What does the Rinnengan allow its user to weild? All of the nature affinities. I think it would be too coincidental to think that the Sage had mastered the affinities, then recieved an eye that granted one all of the affinities. While this is only an assumption, I think it would make more sense that humans being able to control fire, wind, water, earth (Nature) stems from the Rinnengan and when I say Rinnengan I mean the power of the Juubi, and is not something they possesed prior.
I have one more point about the son's, but I'll leave it alone for now..
Anyway, it was a great read, something I can tell you put a lot of creative energy into and I hope you have successfully deciphered Kishi's hints.