I had some controller issues with Mario 64 as well, mostly due to the shape and size of the N64 controller. A few years ago I replayed it with a DS3 controller and it was a much more enjoyable experience, it's an excellent game! It has shown a bit of age though so I'd love to see a remake too!
I hated the 64 controller. Super Mario was one of the handful of games I didn't hate the controls for.