I poked around in a bunch of menus, and found a lot of interesting stuff, but I couldn't find any way to change the controls. I would love to be able to move the shooting button to the left trigger on the Circle Pad Pro, or to the R button. Is that possible? Or am I stuck with having a sore pinky forever and ever?
You can edit all the controls of the game via the Control Configuration menu.
Options > Controls > Control Configuration (step 3 will allow you to change your shoot button)