The SNES controller was perfect for that generation's games. Also, the N64 controller was very much ahead of its time. I used the N64 controller recently, or to be precise I tried to use it. It was difficult to readjust to it. I remember thinking it was the perfect controller back in the late 90's. Maybe the learning curve is higher on the N64 game pad compared to others as it was so different and still is. The 3D stick feels awkward and far too high compared to say the Xbox 360 stick.
The SNES controller is timeless, though!