Board Thread:Theories and Speculation/@comment-32617252-20180403004935/@comment-734582-20180403141525

Jason of the Mangekyou wrote: My explanation would be 'because the eye already exist in the world, maybe that's connected somehow,....or maybe because the eye's are unique and cannot be replicated otherwise madara would've been a rinnegan factory ,-, Orochimaru's loss of arms showed us that the spirit and flesh have a connection, and can exist or be lost partially.

It thus stands to reason that part of Madara's soul is in his (living) eyes, and so cannot be restored by Rinne Tensei. It's possible that the body can only regenerate when a soul is present (Orochimaru's arms couldn't be healed through conventional means), and that's why Madara couldn't.