I've never played Halo (no xbox, you see), but Metroid Prime is awesome... Since I've never played has Master Chief, I shall now come up with a totally ridiculous and biased reason why Samus could beat Master Chief. ^_^
Samus would win because she was made by Nintendo, and Nintendo is just plain cooler than Microsoft (I don't know what company made Halo, but Microsoft made X-Box so... blah.).
T-T