I find it weird that there's no general thread for Kid Icarus.
Anyway, I found the controls to be tolerable, I am left-handed and use the default settings. It hurts after a while even on the first level, unless I'm resting the 3DS somewhere. But it's not like it's unplayable, just a bit inconvenient for a handheld game.
I use auto-fire too. It actually helped me figure out not to shoot the monster with the skull face, because it doesn't do so automatically.
The worst issue with the game isn't the controls at all, to me it's the fact that I can't retry a level at intensity level 9 after dying. I hope that's one of the things they change with the upcoming patch.