Okay, I haven't read through the rest of the thread, so bear with me here...
As much of a Halo junkie as I am, I'm gonna have to say Samus would win. First, she's got more powerful weapons. The Chief's most powerful weapon is the rocket launcher, which only holds eight shots. Samus can have up to, what, 250 missiles? ...each of which is about as powerful as one of the SPNKr's rockets; plus her super missiles, and the various beams.
Moving from weapons to hand-to-hand combat, Samus still has the advantage. The Spartans' MJOLNIR armor weighs about 500-700 lbs. Samus' armor, IIRC, weighs over a ton (2000 lbs) -- and she had to be able to lift it with her bare hands before the Chozo gave it to her. The Chief might be able to flip a Scorpion tank upright *with* his armor, but Samus could just about throw a Warthog at him *without* hers.