First off Bull****.
Zero Suit Samus cannot beat Captain Falcon in a fight.
http://f-mode.planets.gamespy.com/media/scans/f-zero1.jpg
http://f-mode.planets.gamespy.com/media/scans/f-zero2.jpg
From the first F-Zero game, Captain Falcon has feats of his own. IN the game's comic it clearly shows him facing off against a bio-genetically enhanced Dinosaur and killing it with his own gun while dodging that creatures shots as well. Then he is able to handle of couple of generic body guards rather easily in a fight.
And that comic takes place 11 years prior to F-Zero GX. So Falcon has had much more experience since then with bounty hunting missions. Add in the fact that Falcon also faces off against a galactic gang of thieves(Goroh's gang), The Bloody Chain which has conquered 3 planets of their own, A mad scientist bend on world domination, a clone who was made to be his superior, a famous mongule head with endless supply of money and weapon resources, a dark lord of evil, & a time traveling mad man with the intention of destroying the universe.
It is stated clearly in his profiles he has captured an astronomic numbers of criminals and that his body & mind are honed from all his battles that he can survive any situation if needed. His has a scar over his left eye to show that his body has not gone unscathed from his clashes in life. If this was a fight with Power Suit Samus, this would be in her favor, however since this is with Zero Suit Samus, she brings nothing new to the table that Falcon has not seen or faced off against before.
Captain Falcon has the title best bounty hunter in his universe, add in the fact that Falcon has no social life outside of the F-Zero or his bounty missions who have a guy who is completely aware of his surroundings and what his limitations are. Add in the fact 4 years previous in a F-Zero Grand Prix he survived the Great Accident which resulted in the suspension of the sport and with Mighty Gazelle only coming out as a cyborg. His DNA was stolen by Black Shadow, and with Falcon's DNA he decided to make clones who were superior to the original. According the F-Zero X's pilot backgrounds Black Shadow is suppose to be a demon, and how he made Blood Falcon stronger was by adding some of his DNA to Falcon's and add in the psychological effect that Blood Falcon goes bat **** insane when he is around Captain Falcon and wants nothing more to end his life and the fact no clone has killed him yet, proves Falcon can handle super human opponents.
Lets also count in the fact, Captain Falcon has built the Falcon Flyer, & Blue Falcon all by himself. It shows Falcon is no slouch when it comes to brains neither. Add in the fact he is currently developing a 2nd F-Zero machine called the Neo Blue Falcon he is on the cutting edge when it comes to technology. We all know Samus mainly relies on her power suit to help her in missions, while we also know Falcon has no power suit of any kind to use for bounty hunting missions and add the fact the F-Zero universe is infested with super human freaks Falcon can handle himself against this creatures. That also shows when it comes to hand to hand fighting Falcon will be Samus's superior cause besides his gun that what he mainly relies on in a mission.
Samus has a paralyzer, Falcon's gun is designed to kill. So Falcon given his & ZSS weapons has the better gun. While their suits aren't much different, Falcon's uit will enable him to tank more abuse than Samus's skin tight suit will.
The fact is without her power suit Samus, is nothing more than another mark on Captain Falcon's long resume of fights.