Quote Originally Posted by NeoCybercoin View Post
Maybe because they aren't his real eyes. Just like how he always kept on eye shut to use the MS or EMS skills he got from Itachi.
Yeah but then Madara doesn't really have his own eyes either, since he got his MS by taking his brother's eyes too. Maybe the reason is that to use the Rinnengan properly you need Senju DNA/blood, which Madara obtained by taking Hashirama's cells. Nagato had an Uzumaki/Senju body so he would have been OK with it.