I think his transplanted eyes are better. It is Itachi's transplanted eyes which granted Sasuke his EMS. It cured his MS blindness and Itachi was disease struck. A tool is only as powerful as it's user, Itachi's eyes used by Itachi weren't very good against Sasuke.
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Now it would be more easier to determine this if the user who implanted it got Itachi's MS abilities but since Sasuke didn't get Tsukuyomi, I don't really know but I think it is the transplanted eyes. EMS grants PS. Itachi's MS eyes only gets you an incomplete Susanoo.
Itachi's eyes also don't give anyone his skill in Shuriken ninjutsu so all I can say is that it depends on the user who acquires them. Itachi's skill in Shuriken ninjutsu can't be passed on to let's say Naruto who has them. Dude only freaking uses a kunai, can't hype him up to be a shuriken ninjutsu master like an Uchiha.