You got some well thought out ideas there. In terms of the 6 natures of chakra, many combinations can be made to fill in the first 5, but as you mentioned, Nagato was the 3rd path SOLELY due to his rinnegan. As we saw in Madara's flashback,Direct from Narutopedia:
Rinnegan
The Sage(SOSP-) Rikudō Sennin was said to have been the only shinobi to have fully mastered the Rinnegan, allowing him to manipulate all six types of nature chakra. He is revered as one of the most legendary figures in the Naruto universe, and is most likely the most powerful ninja that ever existed. He was so powerful that he created the moon using Chibaku Tensei. Even Nagato stated that his power paled in comparison to that of the Sage.
Other important facts...
Facts about Sage of the Six Paths
Appears in Anime +, and Manga +
Chakra Nature=
Fire Release +,
Wind Release +,
Lightning Release +,
Earth Release +,
Water Release +,
and Yin and Yang +
Classification Jinchūriki +, and Sage
Ok NOW THAT WE ARE ALL CLEAR ON THIS...IT APPEARS THAT SAGE OF THE SIX PATHS IS AN ABILITY OF A PERSON TO CONTROL ALL OF THE ABOVE CHAKRA NATURES AND AS YOU NOTED ITS ONLY POSSIBLE BECAUSE HE HAD "FULLY MASTERED" THE RINNEGAN.
WHAT THIS SHOULD MEAN IS THAT NARUTO, ITACHI, ETC COULD NOT BE 1ST, 2ND 3RD SAGE OF SIX PATHS SINCE WE KNOW NON OF THEM FULLY MASTERED RINNEGAN NOR DID THEY HAVE ALL SIX CHAKRA NATURES UNDER THEIR CONTROL. SO THAT LEADS ME TO CONCLUDE THE FOLLOWING AS TO MADARA'S ACTIONS:
1) he spoke of obtaining the 1st hokages powers (senju clan) because only someone with both senju & uchiha blood in one person could mangage all of the following things...
2) Nagato is the third sage of the six paths only because he possessed the rinnegan, 3) Next he must be able to master all six of the nature chakras, we know that uchiha's are already known for Fire release techniques so he has that one already.
So the question is what other Chakra natures does MADARA already possess?
Hopefully by now you all see the pattern of what Madara is trying to do to make himself SOSP, but my question is who in the Narutoverse is ultimate Earth release ninja (in their bloodline) and what ninja has control over YING & YANG which is the SIXTH (6TH) CHAKRA NATURE???? WHO has already shown themselves to be Earth element users that not already dead (ie 3rd Hokage)? Who has already shown themselves to be YING/Yang masters? What does that even mean?
Last but not least....why is NAGATO'S BODY NOT BURIED IN THE DAM GROUND LIKE A NORMAL CORPSE AND EXCUSE ME BUT WHY HAS IT NOT ROTTEN/DECAYED LIKE ANY OTHER NORMAL CORPSE BY NOW....COME ON!!!!! AND WHAT?! SHE COULDNT CLOSE THOSE EYES???? JUST CREEPY!
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, the SO6P had direct access to yin and yang powers which lead me to believe his rinnegan made that possible. So it is likely the only way to manipulate yin/yang is with the rinnegan.
Oh and btw, it did seem to me that nagato's body was a little more withered than we last saw him, but ya he shouldn't look that good by this time.
Maybe Konan had him and Yahiko stuffed so she'd never loose them xd