Both have their advantages and disadvantages. If I were faced with only having one, I'd probably choose a USB HID-compliant controller interface, as it could still be key-mapped later if need be.
Ok, thanks for the information. The buttons you guys suggested look better than I had envisioned. I didn't have any specific dimensions but I was more looking for something round so I can drill through the side plate vs. something square which I don't have equipment to do properly. :)
Yes - the 6 button controller for Genesis can be used with the GamepadBlock. You can switch to 6 button mode with the button combination "A+B+C+Start+Up".