Looking at this from a semi-realistic point of view:
Samus has unlimited ammo. Master Chief does not.
Samus has lots of energy, but it doesn't regenerate. Master Chief's shields regenerate.
So Master Chief would unload all his weapons, take off a couple energy tanks worth of health from Samus, then Samus would murder Master Chief.
Master Chief's only hope is to hide to recharge his shield, run in for a melee attack, then get the hell out of dodge again. Of course, the chances of Master Chief getting away from Samus is close to none. Samus can roll up into a ball, has a dash move, and can jump maybe twice as high as Master Chief.