If you look at genjutsu, it manipulates the chakra going to the brain. So if your genjutsu is stronger than the other it rewrites. But i always thought sound genjutsu was the strongest. IE shikamaru when he was fighting tayuya. I believe he used regular genjutsu as well to preserve chakra which is a SMART move. Also, i think maybe he used tsuyiomi, because he wanted to make sure sasuke got out of genjutsu. And also with each tomoe/upgrade of sharingan you get to see better so a regular genjutsu wouldnt work on EMS, because he'd see through it. So he has to use his most advance genjutsu aka Tsukyi for sasuke to be under the affects of it. Since tsyuki is visual genjutsu that requires you to look into the eyes. EMS sasuke would of saw through it, but since tsukyi controls space and time its a bit different than a regular genjutsu which just controls space. Thats my theory though.