Hotfeet?
The 3DS also had other factors going for it, it had Monster Hunter, Mario 3D Land and Mario Kart come out for it within the year, the former is a huge seller in Japan and the Mario games sells no matter where it is. On top of that, with Pokémon (and Monster Hunter 4 for Japan) around the corner there's something to keep the 3DS around so it's bound to do well and stay that way, thus keeping interest in the handheld for 3rd parties and consumers. Also, the Vita... Yeah, Sony's just letting it die right now so 3DS almost completely has the handheld market to itself.
The Wii U has to compete with the PS4 and Xbox One (well now since Microsoft finally wised up), whether or not they flounder for a bit at their launch that's still the case and it doesn't have the Mario games to move its units yet and won't for a while. So right now it'll be floundering for a while until it picks itself up and even then it's not certain it'll rise above.