As soon as Nintendo released a demo for Smash Bros., it seemed like technical-minded people rushed to find ways to be able to play the game as it was meant to be played: with a controller. And now you can do it too... provided you have the right tools and don't mind fiddling with the insides of your 3DS, that is.
Yes, this is a mod that will likely void your warranty. But, I imagine the end result will be worth it for those of you that successfully brave the mod anyway.
dekuNukem has an in-depth guide on how to mod your 3DS so that you can use a Gamecube controller on it. Assuming you already have a 3DS and Smash, the parts you'll need are rather cheap, with the total coming in to about 12 dollars. The tricky part is getting to the 3DS's motherboard, soldering various things, and making a circuit board for the mod. It's not the sort of thing just anyone can try unless you already know a little about those types of things, as there are multiple steps that could very well kill your 3DS along the way. You've been warned!
Still, for those of you with the adequate know-how, here's the tutorial. It lists all the steps, the parts you'll need, and has accompanying pictures to boot: The neat thing is that after you're done, not only will you be able to play any game with a controller, the system will still remain portable. It will still look a tad rough, but hey. You win some, you lose some.