Samus because boobs
Now seriously, ScrewAttack sucks big time.
OT: I think it is a very uneven fight, i kinda see where people may be coming to stage this battle, they're kind of ''similar'' icons and sagas i guess (stretching the meaning of similar a lot) but in really i see no chance for Master Chief, it's just like Sonic Vs Mario, they have their similar traits and they were legendary rivals but there's no question Sonic is much more powerful, just like most of these cool what if matches it is impossible to have a ''fair'' fight, it all comes to the same answer: different universes, different realities.
With that being said, yes, Samus would win no contest.