Using a GCN controller on 3DS seems like it would be really uncomfortable. The 3DS, obviously, is designed to be held in your hands, but, if you're using a GCN controller, your hands will be full. That means you'll have to set the 3DS down in front of you and then lean in real close because the screen is too small to see properly at any distance greater than arms-length. It'll be like trying to play the Virtual Boy.
It just seems like a really impractical solution to something that isn't much of a problem to begin with. I know we all love the GCN controller, but the 3DS controls aren't that bad. It didn't take me more than a couple matches to get used to them.