Masahiro Sakurai has confirmed (although not surprisingly) that collectible trophies are returning for Super Smash Bros For Wii /3DS. Revealed thus far is one of Ocarina of Time Link’s pal Saria. Important to note is that this image is from the 3DS version of the game, so we can assume that where a game has a portable remake (Starfox 64 falls into this category as well), those trophies are likely to appear in the 3DS version exclusively.
Trophies, like stages, will be (at least partially) version exclusive with the 3DS getting portable-based trophies and Wii U getting console-based ones. Looks like you’ll just have to get both versions if you really want to spin all those trophies around for a good look.