@carter_esque: While I agree with you that Leon killing generally tougher opponents doesn't automatically make him superior to Agent 47, superpowered monsters are still a good indication of his skill level. Over 300,000 citizens of Raccoon City fell to the zombie apocalypse when it was still fresh, but Leon, as a rookie cop on his very first day, took on the entire city after it had already become totally overrun. To give you an idea of how impossible the odds were against him, Leon was one of the 0.004% of Raccoon denizens to survive the incident. Not only that, but he was going up against Lickers, Tyrants, and a giant alligator, while everyone else fell to regular zombies on the city streets. That is a testament to his quickness, both mentally and physically, as well as general talent over everyone else.
You say Leon has only fought mindless monsters and never went against enemies with intelligence - that is completely false. Leon singlehandedly took on an entire army of virally enhanced super soldiers. The Ganado are superior to humans in every conceivable way by miles, and after infiltrating the island of RE4, Leon alone defeated one of the most highly trained special forces groups across the planet (yes the island Ganado were indeed a highly trained army in addition to their physical enhancements. Saddler even implied that he could initiate a hostile takeover of the entire friggin United States of America with them) So in terms of cannon fodder, Leon generally has a much tougher time. However in addition to the grunts, Leon regularly fights against other highly skilled agents, and wins. Guys like Ada, Krauser, and Chris Redfield all have actual FEATS to backup their status as super soldiers. To my knowledge, Agent 47 takes on strictly cannon fodder.
Fights evenly with president Svetlana Belikova, the greatest military instructor of her entire country.
Stalemates Chris Redfield despite being at a physical disadvantage.
Also, in close quarters combat, Leon has a stark advantage against Agent 47. -- How so? Leon is not a better close quarters combatant than 47 is that claim is a fallacy. I do agree that they would probably stalemate each other in H2H combat as I don't see either party having a clear-cut advantage over one another in that department... and that's if the fight is decided in this manner.
That being, he is an expert knife fighter. -- So what? 47 is proficient with all types of weapons including knives..
Enough to fight on even ground with the infamous special forces veteran Jack Krauser, again, despite being at a severe physical disadvantage (Jack Krauser crushed steel in his grasp and moved in a blur)
All these guys have feats of extraordinary skill in addition to their feats of extraordinary physical ability. 47 has never fought someone as good as Ada, Chris, OR Krauser, and he's CERTAINLY never fought someone as good as Leon.
And if this ends up being a shootout instead of fist fight, have no worries, Leon is a 100% certifiable bullet timer. Can the same be said about Agent 47? I think we can both agree that neither of these super soldiers are really going to miss when they shoot each other. They both have more than enough superhuman accuracy to place their bullets right at the other's forehead - the only difference is, Leon has the speed to move out of the way after 47's bullets are fired.
Agent 47 however, doesn't.
The only thing that I took from your case for Leon as an absolute is that Leon is more acrobatic than 47; a fact that I was already cognizant of. However, how will he be able to utilize that athleticism and "slight" advantage in speed while he's hiding behind cover with bullets flying past his head?? I don't think it will bc I thought that the OP intended for this to be a gunfight but whatevs. I'd say that 47 wins pretty handily with point-shooting which basically locks onto the target. Leon's aiming is manual is makes it faulty (unless the person playing him is an expert gamer or a marksman). With this difference alone, 47 could double tap Leon's skull before he could even react. All of that is pretty technical to game-play and probably shouldn't be used in this debate but it is factual info... not speculation.