....Alright, that is it!!
Lets start with Samus (because it is her proper name), whom is in her Zero Suit. She had toned muscle, and her body's appearance is lithe and light. A smaller mass takes less force to move than a larger one. Samus's legs therefore give her the kicking advantage. When it comes to punching, it can go either way. As the saying goes "The hand is quicker than the eye", and it is certainly quicker than the foot as well. Both could be well-toned for all we know, he can't see either person's muscle tone, except for Falcon's which shows through due to his suit being form-fitting. Being a 'super-athlete ', its no strtch to say that Samus is well-toned under that suit of hers.
She is therefor quicker than Falcon physically. Period. No if, ands or buts. Mass times Acceleration may equal force, but if that acceleration is slower than your opponent, those bulky legs make no difference.
Then lets look at Falcon. He is physically bigger than Samus, and has alot of apparent bulk to his muscle. He also has to keep it tone in order to be truly physically strong. If he is also tone as well as bulk, that can me he is amazingly strong, however, the larger mass makes him slower and therefor puts him at a physical disadvantage in a melee as Samus pelts him with kicks and punches. That is not to say Falcon is defenseless.
If Falcon can manage to grab her, than he could end it right there if she doesn't use the Electrolyzer fast enough. Via a crushing blow to the temple or neck, both of which are fragile areas of the human structure. He could also possibly get off a few punches or kicks off of her, both of which can break bones if they are accurate and powerful.
Samus can kill him if his crotch-cup (if his suit is equipped with one) fails to protect him, as she can kill him by kicking him in the nads and making the reproductive organs rupture, which is possible and an option she has. She could also kill him with the Electrolyzer. She can also kill him via the temple and the neck.
Falcon's gun would be more like an Electrolyzer because just giving him a IRL laser to nerf him is unfair.
[My Analysis]
Body Endurance: Falcon.
Reason(s): Captain Falcon's larger bulk and possible well-toned body can allow him to take more hits from Samus depending on the area he is hit. The less critical areas give him this advantage.
Body Stamina: Samus
Reason(s): Samus' smaller, lithe body takes less force to move than Falcon's does, she therefore has more potential stamina. Falcon's bulky body takes more to move thus he uses (although minimally) more effort than Samus to move his body.
Speed: Samus
Reason(s): This again has to do with lower mass leading to less required acceleration and force to move the body. Samus' smaller body simply gives her the advantage over Falcon (even though the maximum speed for a human sprinter is 25 mph at top speed).
Bodily Force: Falcon.
Reason(s): Falcon's bulky, but probably well-toned muscles give him the distinct advantage of superior overall strength. However, the extra force and acceleration needed to properly use it to full potential deadens this advantage against Samus.
Armor: Draw
Reason(s): This is the only one where I honestly cannot tell you anything on at this point.
Weapons: Draw
Reason(s): Both use an electrolyzer-like gun, giving them both an equal chance to kill if Falcon is allowed to get his gun out of the holster.
Winner: Samus
Reason(s): Both Samus and Falcon have advantages over one another that can throw the match their way, and both have ways to kill the other as well as melee options and long ranges options to choose from.
However, Samus takes the match by a wire due to her lithe body and higher potential physical speed over Falcon. She also has plenty of ways to overcome Falcon should she be cornered somehow. her Electrolyzer being constantly in hand tips every match potentially in her favor.