You may know this from reading the operations guide or from trying it, but in case you don't, Mega Man 9 does not recognize GameCube controllers -- despite previous information leading us to believe that it would. We had yet to try it, satisfied with the Wiimote and the Classic, until alerted by tipster "fatcatfan." We switched on the Wavebird, kept close by due to frequent Chibi-Robo, and ... didn't play Mega Man 9. Confirmed.
This is especially bad news for people who ordered RetroPorts specifically for Mega Man, or who expected to use the Hori GameCube pad. Please don't let it stop you from buying Mega Man 9.