To start.
You completely failed, when you said they cannot use ninjutsu... So what you said would be that they cannot make a bunshin for instance. It's true they haven't shown any specific chakra affinities, which is probably it. But to say that they can't use ninjutsu is bullshit. You seem to base a lot of your theory on this fact, so it kinda blows...
Regarding the Juubis eye. It is not a rinnengan till Kishi says so. Thus stop making idiotic conclusions on this topic. It might as well be a completely different eye that we haven't heard of yet, and you can't overrule this possibility. So stop it please.
Regarding the seal Naruto "used", it was simply due to the way the seal was made. It is of course a pretty valid evidence that it was invented or used by the so6p, which strongly points towards him being from the uzumaki clan as well.
The sage could use ninjutsu, when he traveled the world as a monk, as Jiraya described it. It is clear that at this time he had rinnengan, since jiraya said that he had the same eyes at nagato, when he did this. You say he didn't teach them, but that is false as the manga says otherwise. You do, however, have an interesting theory about how they became able to use ninjutsu, however, ninjutsu have nothing in common with natural energy. Ninjutsu is a specific way of using chakra, and people didn't suddenly get chakra. They had it all the time. The sage just taught them how to use it.
All in all not a "perfect" theory, and there is too many flaws. We can always take the discussion as for whether they can use nijutsu or not, but what I think is the important factor regarding it, is that they have shown no chakra affinities, except for Naruto of course. You should focus on that instead.
As for last there is one more major flaw. Why don't you discuss or theorize how the rinnengan can be awakened by a person that has no juubi or jinchuriki sealed inside them? This is probably the most important fact that the rinnengan cannot be from the juubi. So unless you somehow make a theory that explains it, your entire thread is pointless.
