I've got two dilemmas with Smash Bros 4.
1) Do I really need both versions? (I really want that answer to be yes, believe me).
2) If I only got one version, which to get? Wii U will look amazing and more traditional and comfortable to play. 3DS is portable and something of a novelty, with exclusive modes.
Hopefully Nintendo run a promotion for ordering both, which will ensure I get each.
1. No, but there's likely enough unique content in each to justify getting both.
2. Depends on what you want most out of it. Wii U will probably be the definitive version for multiplayer (if only because of community preference), but the 3DS seems to have a wealth of modes suited for solo play. Smash Run seems to be their biggest push perhaps because it's impossible to make that work on console and still have 4 player MP.