Wow, what a way to start the year. It's neat how there'll be trophies exclusive to each version, but I wonder how they'll deal with representation? Characters like Olimar and Wii Fit Trainer have never made appearances on handhelds before. edit: just reread the Miiverse post and it says 'mainly from handhelds', so there could be exceptions.
Regardless, I'm looking forward to collecting them all this time (still need to get like one or two in Brawl, bloody Meta Ridley).
The exceptions may include anyone from the 3DS titles who appear in Super Smash Bros. U, so Xerneas will probably get a trophy for the Wii U version, thanks to its presence on one of the Wii U screenshots.
However, characters like Dillon and Hades might be less fortunate, seeing as they're currently 3DS-exclusives.