As someone who grew up on Halo and twin-stick shooters, playing Metroid Prime on Wii was a revelation. It offers the satisfying gameplay of a light-gun shooter but allowing you to actually control the rest of your actions fluidly and feel fully immersed in the character. Not to mention how perfectly the Metroidvania level design was translated into a 3D plane, which perfectly complemented those controls.
As far as single-player FPS experiences, I'd say Metroid Prime with pointer is really only topped by something like DOOM at high framerates; but playing DOOM at the proper speed requires you to be somewhat familiar and comfortable with either twin-stick or M+K controls. I can't imagine trying to really rampage through those games with pointer controls or relying on gyro to calibrate your aim. Or at least I've never cared to try it. In DOOM you don't take time to aim, you maim and slaughter instinctively which relies on moving as fast as possible.
Anyway, I'd go with pointer.
