Rinne Tensei and the yin/yang duality.

We all know the quintessential example of Onmyōton: Izanagi. Yin chakra can manifest imagination and form, while yang chakra imparts substance and life. Human beings in the manga are characterized by a body and a soul. We can relate this duality in terms of the same division of form and substance.

When ripped out, Shizune's soul was an amorphous, metaphysical form. Classically, the soul is the concept and identity of a human being. We can relate the soul to yin - that which is the indivisible form separating existence from nonexistence.

By contrast, the physical body, which anchors the soul to the real world and assigns substance that gives a person life, is related to yang energy. We already see that yang chakra emanating from Naruto can bolster the life of plants around him, making them grow. The form of the body, and its health, is the domain of yang.

Rinne Tensei, which returns the souls of the dead, and repairs their body, deals with both. It is Inton in that it manipulates the passage of souls, and it is Yōton in that it revitalizes bodies for which life has ended. Although it may not specifically be an Onmyōton, we can see that it requires a large amount of chakra, likely a large amount of both yin and yang chakra.

Why was Nagato revived crippled, emaciated, and with white hair?

Edo Tensei is shown to revive the person in the image of their soul as they died. The DNA is used to anchor the identity of the soul and to construct the biology of the body (preserving kekkei genkai). However, Sasori, Deidara, Kakuzu, and Itachi were all returned to life in healthy, working bodies far eclipsing their physical state of being at death. What happens when a soul is damaged, exhausted, or drained of yin energy? Using such a soul as a template to reconstruct the living body will create a similarly exhausted body.

The yin aspect of one's chakra is tied to the soul, while the yang aspect is tied to their living body. When a person overuses their chakra, they feel physical exhaustion, and extreme overusage causes death. Most ninjutsu use some combination of yin and yang chakra. We saw this with Kakashi numerous times, including the circumstances of his death. His problems were often associated with overuse of the Sharingan, which is closely associated with yin chakra. What about an extreme case? We saw it again when Naruto appropriated most of the Kyuubi's chakra. Note here that the Kyuubi is missing its yin half, and is thus completely yang chakra. When it lost yang chakra, it became emaciated not unlike Nagato.

Summoning Gedou Mazou changed Nagato forever. Without bijuu, it was fueled by Nagato's chakra, and produced a phantom dragon that consumed souls from the living. In fact, the technique, Genryū Kyuu Fūjin, is written 幻龍九封尽 with the same kanji of the word genjutsu, further corroborating that it is a spiritual force made real. Gedou Mazou drained Nagato of a large amount of chakra to use the technique, causing his frail form. Likely, yin and yang were both consumed from Nagato in large quantities to give form to the dragon as well as power to affect the real world. In turn, both his body and his soul were consumed to give fuel as yang and yin chakra.

Thus, as an extension of the previous postulate, Nagato can no longer use Gedou: Rinne Tensei. After overexerting himself on both Gedou Mazou and the first Rinne Tensei, Nagato was simply a husk. When Madara found Nagato's body, he marveled that Nagato had turned his own hair white - he had exhausted all of his physical yang energy. Furthermore, the hypothesized yin nature of Rinne Tensei had also taken its toll - Nagato had exhausted the energy of his very soul. While Edo Tensei grants him a chakra supply to work with, likely sourced from the living host used as a sacrifice, it did not return Nagato to a healthy form, because in life, he had irreparably sacrificed body and soul.

"With our eyes, we can do virtually anything."

A relatively large panel was reserved just so Nagato and Itachi could make this statement. Doing so served the obvious purpose of hyping Rinnegan/Sharingan Madara, but at the same time, it can also be taken as foreshadowing for some future accomplishment of these two characters. I expect both the former and latter interpretations to play a role in the coming chapters.

Itachi's recent actions suggest a further motive.

Immediately upon regaining his free will, Itachi had the element of surprise on Nagato, but left Nagato alive.

It is well known that Itachi is a very efficient fighter. After being freed from Edo Tensei however, Itachi used several Amaterasu, instead of immediately sealing Nagato. As we know, Itachi can both activate Susano'o and move the Sword of Totsuka at great speed. Arguably, he can do this even faster than he can fire Amaterasu. Why attack the summons individually, and then Nagato, when sealing Nagato would end both him and the summons in a single move?

Rather than permanently deal with Nagato, Itachi chose to disable him temporarily so that he could chat with Naruto. He is also notably absent as Naruto rushes to Bee's aid.

Naruto's soul is the catalyst.

As an Uzumaki, and as the kyuubi's host, Naruto has a large natural reserve of chakra. Of course, as an Uzumaki, he is rich primarily in yang chakra, but that does not of course preclude him from having yin chakra. In fact, by sheer quantity or by some kind of Uzumaki compatibility, Naruto is most likely the best source of yin chakra out of all 3 combatants now facing Nagato.

Nagato's ultimate fate.

At the end of this chapter, Nagato went beast-mode and stole a large amount of chakra from Bee. As he did so, he regained his youth and his health, so much so that he not only shed his physical deficiencies but seemed to reverse in age. We can safely assume that what he obtained from Bee was yang chakra. Thus is healed his body, or his substantive existence.

Meanwhile, his yin essence - the soul, is still damaged and/or weak. By soul-ripping Naruto, he will gain the yin chakra he needs to access the Outer Path. When he does so, he will be ready to use Rinne Tensei once more. The first-born child of destiny will return to the path.