http://xbox.about.com/od/buyersguide/a/vgmosick.htmhttp://en.wikipedia.org/wiki/Motion_sic ... n_sickness
It would seem that you're just unlucky and that Metroid Prime gives you simulation sickness when in 1st person view for some reason. I looked online to see if others experienced it from MP, and indeed there were. It looked like some of them felt better after switching off HUD lag, others were still sick (like you).
Looks like you just need to take breaks by either pausing or saving and quitting.
If MP1 gives you simulation sickness, I bet you'd be 100% nauseated by Mirror's Edge for Xbox360/PS3; that game has a pure first person perspective with no HUD elements (though there is an option for a tiny reticule in the center for point of reference).