Board Thread:Theories and Speculation/@comment-25122992-20170404175224/@comment-27089028-20170406231909

The reason why Madara did not retain the Rinnegan when he became a real living being again is because those eyes were the result of the reanimation jutsu and were not his real eyes which he gave to Nagato prior to his death it's as simple as that. The Rinnegan are incredibly powerful eyes, the genuine article cannot be replicated.