Not intended to be a "which is better...." but rather, what are your overall thoughts on one vs. the other. Are you glad you got both? Will you get the other if you only have one?
I wasn't looking forward to the 3ds version all that much, but caved in and got on launch day.... Have about 25 hours on it- which is a lot for me. I really enjoy being able to play it on the fly as a time killer, plus at the gym.
Waited a week to get the Wii U version. At first wasn't blown away by it- I think in part b/c I've been playing the 3ds version so much. But I've been playing the Wii U version for a bit now too- actually at a faster rate than I was playing my 3ds version (have six hours on it already and got it on Black Friday- but didn't play it until Saturday).
All & all, VERY pleased with both- I got a free $15 gift card at Target with purchase, so I got an Amiibo (Fox). Haven't used him yet. I'll bet that I end up with over a hundred hours of play on these two by April, if not sooner. So, at a dollar per hour of entertainment- likely much cheaper by this time next year (less than fifty cents?).... this was a great way to spend $100.....