I alter the buttons so that games play with the "SNES" input style where Y is action (fireball, etc.) and B is jump. I also add L and R functionality to the ZL and Zr buttons.
Exactly the way I do it. It's the only way to play! It's the reason I don't play 3DS VC games very much at all, as I can't adjust those controls (at least I don't think I can). If I can't play the SNES (or NES) way, then I am forever struggling.
I even have one of those SNES gamepads that connect to the Wii remote. Best thing ever!
I have to agree with people here that the R and L buttons on a game pad are not as nice to use as the triggers ZR and ZL, switching between them is almost as difficult as it was back on the Game Cube controller.