So I checked around for a solution to my problems with this version of SNES9x. Found this on another forum:
it seems that you are using one of Lopst's illegal and buggy versions, which have a weird key configuration. To select menu entries, you have to press button 1 on your wiimote. Button 2 will quit the menu and start the emulator. To go back to the menu, you have to press the home button on a classic controller (the home button on the wiimote does not work)
Using 1 to navigate the menus worked fine. However, once in the game I couldn't get out even with the Classic Controller, so I still didn't get much accomplished. The visuals looked like the same not-quite-VC-sharp, though.