Would he? Naruto has been shown to be an infinitely more perceptive sensory ninja while in Sage mode.
He may be able to recognize Genjutsu instantly in that state. We don't really know yet, because nobody has tried to use Genjutsu on him while he was in Sage mode.
I'd say that's impossible to tell without knowing what other powers EMS gives Sasuke.
If the only thing it gives him is access to his current MS powers without costing him his sight, then yes, I think Sage mode is more powerful than the powers Sasuke has used so far.