She destroyed an entire planet's worth of evil creatures in Echoes... Every game she's in involves Samus vs. a huge freaking army.
The genetics behind Chief have nothing to do with anything, as his entire physical make up was altered to make him better. (You can't train someone before they are born, btw) Samus is the same way, and both have very similar upgrades. (Samus is slightly more agile, MC is a tad stronger, as far as I can tell) Master Chief is a great tactician, highly intelligent, and very very well trained. Samus is also very very smart, and was trained by a race that has perfected war to the point where it is obsolete. Human tactics, as well as technology, pales before theirs. DO NOT underestimate the Chozo.
Samus's suit is much more advanced than Chief's is her weapon is built into the suit and never needs to reload, where MC's guns do. I already stated that in a fair fight, Chief would have no way to use a sniper rifle, as Samus is faster than him in ball form. If he tries to run, she's still got super missiles. Samus's cannon has better range than Chief's throwing arm, plasma grenades won't help much. Chief's shield recharges, but it is fairly weak. A few shots from most of the guns in the Halo world will kill him pretty easy, and Samus's cannon is in no way as weak as the Halo guns.
GalacticStorm keeps saying MC could win cuz he could beat up a woman he finds on the street...