Board Thread:Naruto Discussions/@comment-26488946-20150612205152/@comment-681696-20150612212259

There was no canon explanation for Nagato being unable to use his eyes sharingan abilities nor do we even know for a fact Nagato wasn't able to use his eye's sharingan abilities.

My theory is that Nagato being an Uzumaki is more compatiable with Hagoromo chakra which responsible for Madara's Rinnegan than Madara and Indra's chakra which is responsible for the Sharingan.