I'd say a tie because there are too many variables to account for. Such as, environment, weapons, abilities, vehicles,etc. And other stuff like, would MC have Cortana with him?
Samus's Metroid Prime games have a better single player / storyline but they don't have online (except for Metroid Prime Hunters, but that doesn't even compare to Halo's online) and Halo has top-notch multiplayer. I like Metroid more because the one game with multiplayer is free and is still really fun, and the story modes own halo's. If Samus and Master Chief fought, Samus would win. (See samus's "final smash" in super smash bros. brawl and you will see why) Watch: http://youtube.com/watch?v=umnGPrHmvHE At 1:00, that's why Samus will win.
http://www.youtube.com/watch?v=cL-mR79GErU watch that and find out! LOL thats the video to a paraody battle of what it would be like,its has bad graphics but the guy made it fricken AWESOME. i watched it like 6 times,its great.
Sam Fisher beats them both but MC. Xbox ftw. EDIT: WOAH just watch that video, hotness. MC gets an election (Hehe) and then that?!? Awesome.
You have to read the books then, master chief was trained as a young child in harsh conditions with a group of other special selected for the spartan program, then to top that he was put through a deadly chemical experiment to enhance his entire body to be non-human like, which he made it through, as others because deficient. Also The story line of master chief gives him my vote ^_^ Hes fighting in an epic story line to save the planet earth from a fallen apart alien race and stop a deadly infection from taking control of everything living