As I said earlier, Kishimoto only acts based on logic (sometimes he stretches his logic to reach some conclusions, but he doesn't act without logic).
This said, I agree that Naruto will definitely have some upgrade. But my criticism is that:
- He lacks the DNA to awake a Doujutsu, so he won't awake that doujutsu (until proven wrong, of course).
- He lacks the knowledge/experience to perform Doujutsu techniques (for obvious reasons).
- He didn't have potential to awake a Doujutsu from birth (Sasuke did; Hagoromo did if not born with Rinnegan).
He knows the effects techniques, but there is a huge difference between knowing the techniques and knowing the mechanics to perform the techniques.
I have to say, I wanted Naruto to be totally equal to Sasuke. But when you think about it, Sasuke wields Hagoromo's DNA in his blood, but Naruto doesn't. The Yin part of Rinnegan was inherited by the Elder Son, and as we are talking about inheritance, this is related not only to Yin, but to genetics as well, and the Uchiha Clan existence is enough proof for this statement.
I also mentioned that the Yang of the Eyes of the Sage turned into common eyes, and with the flow of time these common eyes became the eyes of the Senju Clan. So you're not saying anything new, we agree to this extent.
So, answering your first questions... Naruto is someone that handles chakra, in huge proportions, so if he has an upgrade, it has to be related to chakra, not to DNA, and Rinnegan is something related to DNA, Madara is the proof, arguing about this fact at this point would be futile.
Henceforth, you're right about your last sentence: Naruto and Sasuke can't be taken as Yin and Yang, even if (I) wanted them being equal... because their physical properties are totally different. The only possible Yin and Yang for them (in this context) is their philosophy.
This told, it is most likely that Naruto has an upgrade related to body or to chakra, rather than eyes (which properties belongs to the Elder Son bloodline).
Look at chapter 462, and you'll notice that chakra and physical properties are very separated. <<The Elder Son inherited his eyes and his powerful chakra>>
So, telling that the Rinnegan is the final manifestation of the Senju and the Uchiha, you only hold the half of the truth. You should say that the Rinnegan is the final manifestation of "The Eyes of the Senju and the Eyes of the Uchiha". You can't discard the powerful body inherited by the Younger Son, and the common body that was inherited by the Elder Son. These also are Yin and Yang of the Sage's Body.
...think about it. Why didn't Obito turn his MS into Rinnegan when becoming the Ten Tails Jinchuuriki? I really don't see Naruto awakening the Rinnegan if someone who met even more requirements could not.