If your use of Smash 4 will be 100% at home, the Wii U is better.
If you'd like to play Smash 4 while on the bus, waiting for bus, waiting for your girlfriend outside a store at the mall, otherwise "twiddling" your fingers anywhere for X amount of time, then 3DS would kill dead time.
Generally the GCN controller would be a fantastic control option in comparison to the 3DS! But the major problems are:
1. Transportation, no one wants to carry a GCN controller in their pocket, if they can even fit it in the first place.
2. embarrassing, if your somewhere you don't want to be or waiting something out, it'd feel tacky to connect a game controller to a small device, then embarrassing as people stare at a guy with a controller attached to a tiny little screen sitting at a table.