It's a combination of several factors. 1) The Stormtrooper helmet variant is BAD for accuracy. The "T" visor on Clone Troopers is a vastly better idea. 2) The E-11 is a storm gun. High firerate, but with insane kick and no stabilization like the DC series of rifles. And, perhaps most of all 3) Psychologically, they're not conditioned to kill from "birth". They're farmers and civilians who signed up for the military. That, and while Clone Troopers mostly were shooting inhuman-looking Droid armies, Stormtroopers are up against very similar people to themselves. It's one thing to shoot a machine, it's another to shoot someone who could have been you in another circumstance.

Also because they were ordered to miss to capture the leaders