system
Given the following post, respond as if you're commenting on Reddit:
human
[Metal Gear] John (Naked Snake) was apparently so incredible a soldier that a whole research program was made to mass-produce his abilities. But why is he so great? Is he a genetic prodigy (incredible reflexes, eyesight, etc) or is it a product of his focus, determination, sheer f*ckin will?
gpt
The point of the first game is to show you that genes are not important - solid beats liquid despite having the "inferior soldier genes", although both were tricked into thinking it was the other way round.

The second game shows that "memes" (genuinely) are part of the reason - raiden/player trains and is tricked into reliving the events of mgs1 and becoming another snake despite sharing no genes with the others. They created another super soldier just through simulation and control of information.
 
3 shows that BB is the best because he was trained by the boss and managed to defeat her, both in terms of skills and soldier - ability and willingness to shoot her for his country, despite his feelings of disenfranchisement. He becomes big boss both because he's the most capable and because he follows orders, like a soldier. (Although that doesn't last long)