The 3DS has amazing potential. In theory, it can push (slightly) less polygons, but more textures and shaders than the Wii. It even does tesselation, though no games use it (so it might not work well). That potential gets almost halved because it has to do many things twice while rendering 3D. Still, it has amazing potential, and Metroid Prime could look fantastic and work really well with the 3D screen. I'm not sure whether I'd prefer a Metroid Prime 3DS or Metroid Prime U.
The 3DS' hardware is pretty nice, and I do think it reflects the hardware design the Wii U will take. Pick a small box and small power consumption, and squeeze all the power out of it you can get.