By Solid Snake.
In all seriousness. What does Master Chief have going for him? His suit is just body armor and a shield, and he has super strength. He also only has two guns. For conversations' sake, a rifle and a pistol.
Samus' armor can be expanded to near invincibility with enough energy tanks. She also has hundreds of missiles, bombs, super missiles, and many different energy weapons. Moreover she's the toughest bounty hunter in the galaxy, and has made a career out of keeping men at bay. Assuming Master Chief has a penis, he'll be chasing after Samus like the deprived school boy he is, and she'll blast his ass.