The man in the mask is the Senju Clan ancestor
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I believe that "Tobi" is the Senju Clan ancestor. According to Narutopedia, "He inherited the Sage's "body", willpower and physical energy and believed that love was the key to peace."
I believe that him inheriting the Sage's body is what has kept him alive for so long. I think he worked behind the scenes to bring peace to the ninja world through the Senju clan until he realized that there would be no peace. With this conclusion formed, I believe he gave his brother's eyes (The Uchiha Clan's Ancestor) to Nagato as a child. Nagato is a relative of the Senju clan due to the fact that he was an Uzumaki meaning he could use the Sage of the Six Path powers. After Nagato failed and turned "evil", I believe the Senju clan ancestor became disenchanted with the ninja world. That's why he "took back" the Rinnegan.
I believe he has either inherited the "Curse of Hatred" or has lost hope with the ninja world. He sees that his father has failed to bring peace to the ninja world so he wishes to become the Ten Tails jinchuriki, like his father was, to truly bring peace to the ninja world through eternal Tsukuyomi.
I believe the Naka Shrine is the answer to these questions as well.