The Uchiha clan is supposed to be descended from the Older Son of the Sage of the Six Paths, while the Senju Clan is descended from the Younger Son.
As the Older Son he had inherited the eyes of his father's IE: Rinnegan. Not only this but he felt that power was key and domination is a form of power.
Further Tobi made comments that an older brother could not kill his younger brother (He is one of the few key figures in the universe with a brother). And his claim that the Rinnegan were not Yahiko's implies even more so that The Eldest son of the Sage is in fact Tobi.