1. The Sage was just that, a Sage. He was strong enough to withstand Natural Energy, and had the mental discipline to become a true Sage. Just as with Naruto, this reflects more on his strength of character rather than his skill. He was just like Naruto; compassionate, wise, and gutsy.
2. The Sage did not need the Rinnegan to fight the Juubi; all he needed were Sealing techniques and Sage arts, both of which pre-dated what is known today as Ninjutsu. Written Seals were able to be activated with chakra, without humanity being able to actually perform complex handseals or manipulate the Nature/Shape of chakra. These were powers undiscovered until after the Sage absorbed the Juubi and unlocked its understanding of chakra, which he could then teach (at least to the extent that regular humans can perform it).
3. The Sage gained the Rinnegan from the Juubi, and also knowledge. The Sage could create life, but also apply the knowledge of Yin/Yang to comprehend the basics of every jutsu. He believed bestowing this knowledge could allow humanity to better itself. He probably didn't intend for it to be used to create a military system, but rather for practical applications or self-defense.
4. The Mokuton, as we know at this point, is the Juubi's power of creating life. It creates plants in the absence of the Yin (mental) counterpart from the Sharingan, but when combined, the complete "Yin/Yang" techniques can create animal life as well. When the Juubi spawned its "Zetsu-esque" army, it revealed its power to create living beings on a whim; these creatures are a more natural / primal version of Zetsu, as Zetsu was meant to be an artificial human and was created using a human's mind. I don't really view the Mokuton in terms of Wood Element, I just view it as raw Life Force manifested into a technique.... all of its unique properties stem from representing the highest level of mastery over life force, hence why it can grow to such massive scales instantly and can absorb chakra, as well. It awakened in Hashirama because only he had achieved the pinnacle of Senju phyiscal energies (and thus maximized the Yang power of the Juubi that had been handed down through that clan).
5. On the topic of this current chapter, Kishi is being lazy.. he can't conceive of ways for every character to shine if they all perform at their highest capability, so he dumbs some down, makes others more powerful, and has others simply stand aside.