I own Metroid Prime 3 on wii. I agree, it feels very natural, and is quite pleasant to use. But as an avid multiplayer FPS gamer, I can tell you instantly why your idea of using the wiimote fails.
Boot a Metroid Prime game on you wii, load a game, and do a 180 degree turn.
Go ahead, I'll wait.
Did you notice? It took several seconds to rotate 180 degrees, and another second to recenter your aim. That's why your argument falls apart. Mouse-using players can achieve 180 degree turns in literal fractions of a second, depending on individual skill and current mouse sensitivity. And because the crosshair is always in the center of the screen, you're centered already and you may fire at will. A learned habit of every multiplayer FPS gamer is to continuously check their six. This means 360 degrees of sum total rotation, every couple of seconds. You can't achieve that with the wiimote controls of Metroid Prime.
Which isn't to say it wouldn't be possible to achieve better control. Imagine a thumbstick on the wiimote that controlled orientation (and could be depressed to act like a secondary button). Change visual orientation rapidly with sufficient fine-tuning and waggle the wiimote to control the crosshair.