In accordance with Nintendo Director Masahiro Sakura, the Wii U and 3DS versions of Smash Bros. have different trophy sets.
Sakura posted on Miiverse:
“Happy New Year! Pic of the day. There will be trophies in the 3DS and Wii U games, and each version will boast different types and models. The 3DS trophies will be mainly from handhelds and the Wii U version will feature trophies from the home-console games.”
Let us know what you think of the different trophy sets for each console.