dekuNukem has modded his 3DS in order to play using a Gamecube control pad, here is a quote from the source:
gc3ds is a 3DS modification that allows user to use Nintendo GameCube controller to play any games on Nintendo 3DS consoles. This open-source project uses an Arduino Nano to read the state of GameCube controller, then mirror them to Nintendo 3DS with a maximum delay of no more than 1/1000 seconds (1 millisecond). Users can also choose to customize button mappings between gc controller and 3DS with a LCD screen.
Here are some videos of the mod in action:
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