Big Boss absolutely beats Captain America down. Anybody who actually reads comic books and isn't a fanboy can see his combat ability is far superior. Who are the typical Cap antagonists? Crossbones and Baron Zemo? Maybe U.S Agent or Nuke or someone like that? The antagonists in Metal Gear are like an amalgamation of all the best assets of Captain America's villains. Never before has Captain America even *encountered* an opponent like Gene, who COMBINES speedster powers with super soldier combat skill. I've never seen Captain America get pitted against a Metal Gear, he's never proven he can keep up with something that overwhelming, whereas Big Boss has.
Just look at a somewhat recent Captain America villain, John Steele. The whole idea behind Steele was that he's a stupid bully with no fighting skill to speak of, he's just a big strong goon. Not any bigger and stronger than Colonel Volgin though, yet Volgin was also a talented fighter in his own right with LIGHTNING powers added on top of everything else. Now John Steele straight up defeated Captain America in a fist fight, his physical advantage was just too much, yet a less experienced Big Boss defeated Colonel Volgin through sheer skill.
It's simple really. Big Boss beats better opponents, faces more dangerous odds, that makes him the better fighter.
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