My example is BC Kid. A fine PCE port and a very pure platformer. There is a joystick control with "up" and a pad control with a second button for jump.
Well, both controls works fine. I cannot make a clear preference. It depends on how good they've made the controls for a game. Yes, Mario is a good example for smooth and decent pad control, but i have also played a lot of console games with a bad jump control (delays, inaccurate..). This happens in shitty Amiga platformer too.