I think using a joystick was a great idea, as it brings more precision. I generally would do a slow sweeping motion while firing to clear out some of the enemies, which would feel awkward with a spinner.
As for the NES version, I have nothing to tell, as I haven't played it yet.
I will agree with Lynxpro on the Xbox Live Arcade version though, it's by far the worst Gyruss version.