What gamepad were you using, and what browser (and OS)? The gamepad support isn't very great right now since there are too many different gamepads (and even different Xbox-like gamepads - that in theory should work in an identical way - act differently on the same browser) and every browser has a little different gamepad API implementation (for example, Firefox thinks dpad has two axes, Opera consideres dpad normal buttons)
I played the game through with my gamepads on two different browsers, and it worked fine, so in theory it should work with Xbox-like gamepads...