The 3ds version is more portable, and usually cheaper.
The Wii u version has better quality, it has that special board game
mode, and Crazy Hand mode on it. Also, you can connect a few different
controllers to it for more play styles.
The main solo Master hand mode is also different in both versions.
Personally I like the 3ds because I can take it around everywhere, Easy to travel with.
But the Wii u version has more content for you, especially when you're playing alone.
I know this thread is old, but I hope it helps someone :3