Well i for one see 3 ways that a transplanted eye might work:
1.the eye has the ability to turn into MS (original user awakened MS) but when it is transplanted into a new body it is in a regular 3 tomoe state (not MS). In this case the new user would be able to use both regular Sharingan, and MS since the eye already has that ability... Danzo's case...
2.the eye is just a regular sharingan, and the new user that gets it, advances with it, and awakens MS on his own... Kakashi's case
3.the eye achieved its final form (lets say rinnegan) and when it is transplanted it is done while the rinnegan is active, not the regular 3 tomoe sharingan, therefore the new user doesn't have the ability to go down a level...(like revert back to EMS, MS, regular sharingan) hence why Nagato only used Rinnegan jutsus and no sharingan jutsus.
It's just a theory... and for now i find it the best reason to why Nagato didn't use any sharingan abilities...
Hope you get my point of view...