It's honestly not bad once you map the buttonsGlad I copped the N64 controller last year. I couldn't imagine playing this with anything else.
Framerate is much smoother and seems locked at 30 fps. Not ideal but MUCH better than the original
I did it on the pro controller and the joycons.
Since you got the n64 controller you're good, but if you ever want the joycons to lie on the couch or whatever. Here is a decent configuration. I even tried it with Mario 64 and major mask and it's pretty good.
Although for 007 I doubled up on the B button, I can open doors with L while using ZL to aim and ZR to shoot and change weapons with R