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sc94597 said:

Samus' Beams

Long Beam

Spazer Beam

Wide Beam

Wave Beam

Ice Beam

Plasma Beam

Charge Beam

Dark Beam

Light Beam

Annihilator Beam

Nova Beam

Hyper Beam

Phazon Beam

Suits

Ped Suits

Phazon Suit

Power Suit

Varia Suit

Omega Fusion Suit

Gravity Suit

Visors

X-Ray

Thermal

Echo

Dark

Power Ups

Screw Attack

Space Jump

Speed Booster

Morph Ball

Bomb

Boost Ball

Grapple Beam

Grapple Lassle

Grapple Voltage

Gravity Boost

High Jump

Power Bomb

Power Grip

Spider Ball

Spring Ball

Missiles

Super Missile

Ice mIssile

Seeker Missile

Diffusion Missile

Also she was trained for combat since the age of 3 by the chozo. SHe has both dna of the chozo and metroids hightening physical strength and stamina. Oh and most of these powerups and weapons, have the same abilities of the previous when upgraded, so she basically has all of the links I posted. 

Other people in this thread already nailed down why gorden freeman is better. Then the only thing master cheif has is his suit which both samus and freeman also have and you could argue samus' is better, and is physical abilities hightened because he is a spartan. So that is why. Hope I didn't take too long.

Edit: ALso she could control her ship using her suit.

 

You forgot bewbs.