Okay, I think tsukuyomi is being underestimated a bit here. It doesn't just incapacitate, it can also kill if itachi so chooses. He has killed two people with it: his girlfriend and his uncle. Kakashi didn't die because itachi didn't want to kill him and sasuke broke out of it because itachi weakened the genjutsu significantly.
I initially also thought kotoamatsukami is the better genjutsu until I noticed its flaw. If the victim notices that koto was used or if others were around to tell him about it, kotoamatsukami would be seemingly dispelled or at the very least its effect would be drastically reduced. This is shown with mifune.