Board Thread:Theories and Speculation/@comment-25122992-20170404175224/@comment-734582-20170404191142

His eyes didn't Rinne Tensei because of his soul.

You see, we know from Orochimaru that the soul corresponds to a body part: When Hiruzen cut off the soul in Orochimaru's arms, the arm withered. Madara's Rinnegan couldn't be Rinne Tensei'd because that piece of the soul was missing, because it was still existing elsewhere.