Snake is confirmed to be metahuman; his strength, speed, and agility are all greater than Batman's by a good bit, especially striking strength and combat speed. He's bullet timed numerous times from several great marksman (Meryl, Olga, Ocelot), escaped the blast radius of a tank shell after it was fired, and was capable of seeing and reacting to a hypersonic blasts in his old age from Crying Wolf, not to mention successfully evadingnumerousblasts from Fortune's Rail Gun in a tight space for several hours while in his prime (I don't think Batman has mach reflexes). Perhaps most impressively is how he can avoid turret fire from an army of Gekkos simultaneously while taking them all down with the same Rail Gun, effectively absorbing several tons of force into his arms without a stutter. Going with that, Snake has caught a full grown woman falling from several stories up with his bare hands, and has lifted a jeep to free himself and Meryl from underneath it.
Those are good examples of what a genetically engineered super soldier can do, but what really clinches it for Snake is his abundance in actual combat-oriented feats.
Snake's fists do more damage to Liquid than several RPGs did
A fight with Solid Snake has the Cyborg Ninja on his knees gasping for breath
Both are highly commendable showings of skill as well. Liquid Snake was designed to be superior to his brother in every way, but despite an extreme physical disadvantage, not to mention suffering from severe fatigue, David's more advanced technique and higher experience allow him to defy the destiny they were both born to (nature vs nurture is a common theme in the series)
Gray Fox is of course a bullet-fast, 100 tonner. He's the only agent of FOXHOUND to ever earn the codename Fox in the organization's entire history, so he's basically equivalent to Ra's al Ghul in that department, yet Snake's instinct and skills of adaption shine through once again.
In combat speed, Old Snake has supersonic reaction time, and Young Snake takes a shit on Old Snake. He's taken down a whole enemy squad in the time it took Raiden to walk down a hall, cleared a room full of hostiles before Stillman could get out a single sentence, and even blitzed Meryl Silverburgh, who of course was dodging point blank Assault Rifle fire (Snake>>>gunfire)
His physical advantage is vast. Every hit inflicted will completely jar Batman, whereas in contrast, the detective will struggle to even injure Snake at all, who's taken hits from 100 tonners and survived a kick from Metal Gear RAY (the same kick destroyed the entire platform Snake was standing on, so Snake's face>>>iron and steel). Of course my favorite instance is when Snake dove 300 feet off of Arsenal Gear into the water below, out swam a giant robot, placed a tracker on his brother, swam through 20 miles of ocean and sprinted several more all the way to Federal Hall without even being out of breath, all in the time it took Raiden just to beat Solidus. For the record, the average human can't dive more than 90 feet without breaking bone. Stamina, durability - and definitely pain tolerance, all go in Snake's court.
Now, all that said, people still like to claim Batman can win, for the sole sake of him knowing 127 different martial arts, as if that actually matters. CQC is a broad fighting style that focuses on disabling your opponent, and ending them quickly. It makes use of strikes, holds, grapples, and throws, utilizing the users superior strength to great effect. The only problem for Snake is, he very rarely ever fights anyone who he's actually stronger than. Now don't take that as a diss on his strength, he's still the second/third strongest human being on his entire planet. It just so happens that, in his line of work, Snake's standard foe is a supernatural monster or robot. In his world, Snake's combat talents literally qualify as a superhuman power. Batman can't beat people like Gray Fox or Vamp, yet Snake has stomped them both.
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