Board Thread:Naruto Discussions/@comment-26488946-20150612205152/@comment-734582-20150614124505

Remember that Nagato also did not use Limbo, neither did Obito. I think it's simply a case of the eyes being transplants and so, require to be *ugh* "tamed". That is, it takes time for the user to bring the eyes fully under their control, and even then may never achieve this.

Lastly, Nagato was likely not aware of it's Sharingan heritage. An alternative is that it requires the ability to deactivate your eyes in order to switch, but if he got the eyes as Rinnegan, he would not be able to switch. Kakashi got his eye as a Sharingan, and awakened Mangekyou on his own so he could switch that.