LOOK, I'll tell you who I prefer, Gordon Freeman, he is a much more badass character, smarter than John and much more intuitive.
But... I can't ignore facts, in a one on one fight Master Chief would win. Master Chief is a engineered super soldier, with heavy power armour, a rechargeable shield, years and years of hard battle experience and has survived odds that are seemingly impossible (like boarding an enemy spaceship and getting to the high council by himself!). Gordon Freeman has a hazmat suit, a crowbar and a gravity gun which would help against grenades and rockets but not bullets.
So master chief
So less main characters, here's a nice enemy battle
Big Daddy (Bioshock) or
Handy man (Bioshock Infinite)