In 590 discussion I pointed out that Itachi and Shisui were the only two Uchiha not participating in the Uchiha rebellion. I find that very interesting. Why? The rebellion was a setup with Madara as orchestrator. Itachi and Shisui were the only two known Uchiha of the mangekyo level from their generation prior to Sasuke growing up. Either being of the mangekyo level made them powerful enough to be unassailable by Madara's manipulations or being of mangekyo level; Madara found them to be the only Uchiha he could respect after his percieved betrayal and weakness of the clan after choosing peace and clan harmony with the Senju. Out if respect he did not manipulate them with the others.
The Uchiha have power to change reality and destiny with izanagi and izanami. Mangekyo allows some, like shisui, to bend the will of of individuals and groups. Only the strongest uchiha would Madara think deserve to keep their free will and maintain ownership if their destiny after all others accepted growing weak in peacetime afforded by his supposed death fighting hashirama.
Danzo at the kage summit proves it doesn't require much to steer large groups into extreme directions through manipulations and powers of sharingan. I also bet Madara manipulated danzo as well, as insurance and counter pawn necessary for an ugly and nasty rebellion. I doubt Madara respected danzo's desire to acquire uchiha eyeballs and so used ironic justice in subjugating him into his grand scheme.
Again, out of respect for Itachi's genius level and remarkable uchiha power, he let him keep the leaf and his brother. There was also sentiment at play given that Sasuke is analogue to Madara then Itachi probably reminded Madara of his own brother. Or, since Itachi is bad ass, he used the eye he just received from shisui ON MADARA LOL. He used it on him to force his intentions away from the village and sasuke. Kotoatsumaki is awesome, even mafara falls for it. Just a likelihood is all. Takes 10-13 years for shisui's eye to reset for another use? That's about how long it took for the masked man to resurface, probably smarting for having been hoodwinked by itachi into not touching leaf or sasuke. Now he is aiming to hands fully on both.