i've followed both series somewhat intently, until recently, when the real world reminded me that i belong there. if there were to be an actual showdown between the two, which i would weep if there was, heres what would happen.
Samus has no sense of tactics or stealth, which the master chief excells in both. so while she would be expecting him to charge out into the open like every enemy she's ever experienced has done, he would be 2 kilometers away with mines already planted and a sniper rifle trained on her head. she would end up dead before she ever found out where he was. now i'm not a halo fanboy by any means, in fact i had spent years fighting against it's proclaimed GOD like status. but i'm putting this into a sense of realism, if there can be such a thing given the subject(s) in question.
As for LordOmnit's comment of the size of MC's sniper rifle, in the game, it fires 14.5mm armor piercing, fin-stabalized discarded-sabot rounds. 14.5mm is fucking big. 20mm were used in World War 2 as anit-aircraft guns. and Sabot rounds are full of burning magnesium, which is around 6000 degrees fareignheight. this isn't a small rifle, nor weak by any means. one shot and Samus's environment suit would be bubbly and melting. if she can't go through lava, she can't take sabot rounds, period. the assault rifles in halo fire 7.62mm rounds. i've seen what 7.62mm rounds do to people, it blows them in half, literally.
If i had to pick a near ideal woman, Samus is damn close. she's a warrior woman, i find ferocity hot and they are traditionally demons in bed. but if you want an actual probable result of a confrontation between the two of them, what i wrote about would sum it up. the chief isn't anything overly special, he's just a master of his domain, and combat is where he lives. samus is a bounty hunter and mercenary, not a professional soldier. tactics and forethought ultimately win the day in a combat situation, and he's got that advantage by a landslide. sorry dudes.