Madara was the history specialist.
Nagato could be pure Uzumaki with some relationship of Senju.
Whereas Naruto was not pure Uzumaki, still had certain unique things. (refer to when Naruto met his mother.)
Therefore, Madara had chosen Nagato to have the rinnegan eyes.
Also, for Madara to choose Obito, with certain unique things.
Madara took years to plan after losing to 1st Hokage Hashi.
He had to knew the Shinobi history, and certain issue on SO6P.
Madara could instigate to certain Uchiha to revolt, so as Konoha Elders to kill before they do.
Possibly Madara knew this would come, because none of Uchiha listen to him.
Also if any Uchiha alive, he may had problems in killing his own clan.
So as not to repeat the history.