EMS doesn't make a ninja overall better. They can't see better than a MS, they can't move faster, they aren't stronger, etc. All EMS does for them is increase ocular powers meaning Ameterasu, Tsukoyomi and Susano'o are upgraded.
We've already seen from the Kage fight, Gaara vs Sasuke, A vs Sasuke and Bee vs Sasuke that those 3 can be countered.
Ultimately, it would come down to Susanoo battle, which Sasuke would obviously win since he can use that technique much longer than Itachi.
Like I said, Susano'o wasn't the only thing upgraded. Itachi was already a master at genjutsu. Even his MS genjutsu was on a whole new level with Izanagi and Izanami. Sasuke may have an upper hand on Susano'o but same goes for Itachi, he has the upper hand on Tsukoyomi.
With Tsukoyomi, Itachi can disrupt Sasuke's chakra over and over, causing Susano'o to collapse continuously, giving Itachi the opportunity to get within close quarters. We all know Itachi was a better fighter in taijutsu.
Lol itachi cant beat sasuke anymore his sharingans tecs will be useless.
Susano'o's perfect defence doesn't include being able to counter ocular genjutsu. Itachi only needs eye contact. Also, what we've seen from Kakashi vs Itachi was that Itachi doesn't even need Eye contact. He can use other objects with enough lust/shine to it to reflect the genjutsu.
