I've only played the Wii U version so the Wii U edition!

i always played the wii u version and 3ds version does not porform well at all.so wii u better:->

only thing that's better on 3ds is the bigger map (2016*2016 on 3ds and 1024*1024 on wii u) other than that wii u is way better at everything else

i love the jank controls of the 3ds version

wii u has glide minigame so wins by default

Wii U is infinitly better, but I like that I can play Minecraft on a handheld as small as the 3ds.