Wii U. Control options and 8 player mode with better online.
3DS: I'd say Smash Run is better than Smash Tour. But Wii U still has Event Matches and Special Orders. 3DS has 3D visuals, but not everyone is a fan of those, and there are some points where the 3D is really pretty (often at win screens at the end of matches) but other times when it's just a hassle (often during gameplay).
I'd weigh in for Wii U, but if you travel a lot, or know friends with it on 3DS, it's not bad to have on 3DS either. If you have both systems, smash brothers portable and smash brothers full are both fun. And gets you a free Mewtwo.