Every character will run at 60 FPS in stereoscopic 3D, but assist trophies and Pokémon can't.
The 3DS version of the new Super Smash Bros. will run at 60 frames per second.
The whole game will run in stereoscopic 3D. Some assist trophies or Pokémon will run at 30 frames per second, but these will not affect the fighters' frame rate of 60 FPS.