The manga makes it plenty clear that Sasuke can/does not use Tsukuyomi. Both his eyes have powers related to Amaterasu only. But why? Madara and Kakashi could use Kamui using Obito's eyes and Danzo could use KotoAmatsukami using Shisui's eyes. Then why not Sasuke? We have seen that during fight with Kabuto, he uses ordinary sharingan genjutsu on Itachi when freeing him from Kabuto's sound genjutsu.
Does this mean that once you achieve your own MS powers, implanting someone else's eyes does not grant you their power but just give you EMS?
Does the eye transplant work differently for non-Uchihas, as in they just gain the original eye power?
But this still does not explain Madara's using Kamui.
Edit: People seem to be confused about the fact that Sasuke can NOT use Tsukuyomi. Here is the detailed answer I wrote: https://anime.stackexchange.com/a/15018/9123
Here is a Tsukuyomi wiki that clearly states the only user is Uchiha Itachi