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Itachi trains and is like a perfectionist. He's encountered people using genjutsu sasuke on the other hand hasnt underwent genjutsu other than his brother
Sasuke did see through illusion of Shee, and pwned him with his own Genjutsu later. Also, he didnt have problems with standard Itachis illusions. Thats why I believe with EMS he wouldnt have much problems with Tsukiyomi.