Board Thread:Naruto Discussions/@comment-26488946-20150612205152/@comment-4912646-20150613015938

Even Madara himself didn't use any Sharingan abilities while his Rinnegan were active. Instead he (or his wood clone, to be precise) purposely deactivated his Rinnegan when we wanted to cast genjutsu. It seems the only ability shared by the Sharingan and Rinnegan is seeing chakra, which is something all known dōjutsu are capable of. As for why the highest form of the Sharingan seemingly cannot use its most basic "Dōsatsugan" and "Saimingan" abilities, that's anybody's guess.

As for why Nagato couldn't use Susanoo, it is awakened when you unlock the powers of both Mangekyō Sharingan, but doesn't actually require the eyes to be active. So it is presumably impossible to gain Susanoo by transplanting somebody else's eyes, except in the special case of Obito's spirit entering Kakashi's body. Then again, we saw characters consistently activate their Mangekyō whenever they used Susanoo for hundreds of chapters, so there must be something more to it we haven't been told.