A lot of people here forget that Chief can only have one type of weapon, or 2 single hand weapons. He is not able to carry both a sword and a rifle. Samus constantly has access to all of her weapons. So if Chief gets a rocket launcher, he ONLY gets a rocket launcher. If he has a sword he ONLY has a sword. In case #1, Samus also has missiles, as well as a lot more health. In case #2, Chief won't be able to get close to Samus without some kind of guns for distraction.
Samus's suit is skintight, but it doesn't have holes... Lava and the like would kill her if it did. Bullets are obsolete in Metroid. They will do nothing. Most people here are undercutting Samus's armor. 15 energy tanks takes a LOT to drain.
Cortana is not usable because A: She's a sentient mind outside Master Chief, and B: Samus has her own hacking abilities, and it is close enough to impossible to tell who's is better. This has been gone over.
As to Spark Shine and Screw Attack, Chief is not dodging something as big as Samus from a few feet away. I wouldn't have Samus using either unless it actually came down to a melee fight. Outside of that, If Chief tries to get clsoe he gets blasted.
Samus has more than enough experience not to get beaten by brains alone.
Jedi's don't have armor. A lightsaber could block a bullet perfectly fine, that's not even an issue. But a wide spread shot would be hard to completely deflect, so some of it might hit the Jedi's body directly. Completely different from Samus.