Inside, no difference at all. You can still use all the buttons and circle pad on the 3DS itself after this modification.
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Back, when you want to use GameCube controller, plug in the microcontroller, gamecube cable, and an usb cable(for power) and start playing.
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Like this
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When you're done simply remove the microcontroller and gamecube cable to make it just as portable as before. (although with an empty circuit board in the back)
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It also comes with a LCD screen. Normally you leave it out, but when you want to change button mappings you can plug it in and change the mapping on the fly with your gamecube controller.