The Dual Shock is the greatest innovation in controllers. It's very comfortable and snug in your hands, the sticks are easy to get to and move around.

More recently, games have been embracing use of the right analog which can be disruptive as it forces your right hand to do a lot of multi-tasking. It takes a while to get used to for FPS in particular.

My second vote went to N64. It's different, it's funky and it worked.