One controller generally considered to go hand-in-hand with the Super Smash Bros. series is the GameCube pad, which many still use in the most recent home console releases. Of course, it'll be possible to continue that tradition with the GameCube Controller Adapter for Wii U, but it's not an option for the imminent arrival of the 3DS entry in the franchise.
Not unless you're willing to do some modding, which rules out 99.9% of 3DS owners, we suspect. Perhaps as a follow up to the 2DS GameCube controller mod from earlier this year, or potentially using different methods, we have another mod for using the famous controller on a 3DS system. This time around the modder in question, DekuNukem, has posted instructions on what's required to make it happen; expertise and around $12 in parts, in basic terms.
It's not advisable to mess around like this with hardware, but it's fascinating nevertheless to see what a basic circuit board and parts can do. For the vast majority this is not a good idea or particularly worthwhile, but it shows how far some will go to enjoy their preferred controller on the 3DS.
You can see it in action below.