The thing is we're assuming he didn't die. And we're comparing the feats.
Naruto has ways to avoid Amaterasu, but once it hits him, he's done for it. Also, Amaterasu's ignition can't be sensed through SM. It can only be seen by chakra build up using dojutsu like Obito did, or by seeing the blood in the eyes like Raikage did. Also, if Naruto avoids eye contact with Sasuke in order to avoid genjutsu, he won't be able to see Amaterasu. If he tries to see Amaterasu, he'll get genjutsu'd. So Naruto can't really do anything in this situation.
Also, Naruto's strongest attack in SM i.e. FRS easily gets tanked by Susanoo. Plus, you can only stay in that mode for like 5 minutes which is nothing. If you haven't prepared clones in advanced, you're screwed. And no one will allow Naruto to sit down comfortably and gather natural energy. SM is inferior to MS in every way. MS > SM. However, KCM can put up a competition for MS with it's abilities and better potential. KCM = MS. BM = EMS. BSM = EMS w/ PS.