I don't think anyone can resist a genjutsu powered by the juubi. With that kind of power even an E-Rank jutus goes A-Rank let alone something as powerfull as tsukuyomi. Besides obito wouldn't have implanted Itachi's eye into sasuke knowing he could resist it. And itachi went easy on sasuke even zetsu and obito confirmed it. It took a while for sasuke to know he was in genjutus if itachi wanted to he could have killed him at anytime during that period. tsukuyomi is perhaps one of the most powerful jutsus in narutoverse.
Obito may not know that EMS can resist IT. It's not like he could test that theory.
Obito also has a tendency to just assume people are loyal to him imo. He just seemed
shocked Pain, Konan, and Sasuke betrayed him.
Yes, Itachi was going somewhat easy on Sasuke but not
that easy. He's whole strategy was to make Sasuke run out chakra, so he could defeat Orochimaru when it came out of the curse mark. That and just resisting tsukuyomi with just a 3 tomoe sharingan is quite the feat whether or not Itachi was going easy on him.
Also, perfect jin supposedly can resist any genjutsu.
Finally, Jirayia said any genjutsu can be defeated, right?