Tbf it was always gonna be hard to make good fps controls on the N64 controller. The movement itself was fine once you got used to it (including strafing etc), but the real sticking point as you mentioned is the shoulder button aiming. It pretty much forced you to stop dead to aim accurately. So you really had to pick your time to hold position and take a few shots before running again.

I still had a lot of fun with it despite knowing there were better options out there with mouse and keyboard (although come to think of it when I was first playing wolfenstein and Doom I think I played with keyboard only back then).