The boss kicking snake's butt at all has always been another one of kojima's feminist fantasies.
She has no super powers, she is pretty old and the only excuse you can make up for it is that snake is holding back because he does not want to fight his mentor.
Meryl, Sniper Wolf and Quiet are characters that are somewhat believable, strong but all with their own flaws. The Boss is just feminist propaganda all around, even if you take into consideration Metal gear's anime tendencies that tend to minimize the physical strength gap between man and women.
They developed it together. They are supposed to be on the same level of skill more or less, but somehow snake is completely owned twice without any particular reason. Like watching a black belt fucking up someone who started sparring a few months ago, only to magically be able to beat her a few weeks later, because reasons.
It would have been more coherent with the story if they actually showed the two of them standing on equal ground in the in their first fight, with the only thing stopping snake being his feelings towards her.
You put a bunch of unrelated shit together that has no bearing on what I said.
Boss has a lifetime of experience and is much better at martial arts than Snake, who is a greenhorn who was TAUGHT CQC by The Boss. Him hesitating and pulling back is one factor, the other is that she is just better than him. What is he going to do, shoot her? Good luck, she disassembles his gun at the start of Operation: Snake Eater, remember?
Out of all the things in MGS that don't make sense, people cling on to this because it hurts their fee fees that arguably the most important character in the entire franchise other than Big Boss and Solid Snake themselves is, indeed, powerful and skilled at what she does? Franchise tourism at it's finest, it's almost as if The Boss pretty much founded the modern concept of a Spec Ops unit with her men, alongside an entirely new martial arts technique and all Snake is at the start is another greenhorn that can barely keep up with her. Oh geeze, I wonder who will win in a straight up fight?
It both makes sense and fits perfectly thematically that she is the final, well, boss and only by the end do you actually have the tools and skills to take her down. The pupil surpasses the mentor, this is like writing 101. Do people complaining about these things even consume media or do they just look for outrage clips/reviews and parrot whatever /v/ has to say?
I want culture warriors away from my videogames, I will take all the woke shit in the world(for games I will never play anyways) if it means you lot just fucking leave.
Villains building big ultra mecha robots to take over the world? Clones? A guy posessing another guy through a transplant in his arm? Nah, those things are all totally cool and realistic, but I draw the line at an experienced woman who fought in tons of wars and even pretty much developed the whole CQC system just because she beat a man a couple of times before he actually takes her down to finish up her story. No wonder nobody with an actual brain takes people like Synth or the previous poster seriously when every single "powerful" woman nowadays is a feminist plot to.. like... make women look cool or something.
Metal Gear was never realistic, this is something only a novice to the series would ever claim so you're wasting your breath by pointing all this out. The Boss could manhandle Snake like Senator Armstrong with proto-nanomachine aided muscles as metal music blares and it would still somehow fit in with this wacky universe. Even in MGS3 alone you got a literal ghost stalking you in one of the later boss fights, a guy who can mentally control hornets and turn them into a machine gun, a big russian bastard that can control electricity like Raiden from Mortal Kombat, and the Shagahod makes absolutely no sense itself if you get into the gritty details on how it's supposed to work. Only reason why someone would have a hang up over something that pretty much nobody else over the last 20 years has, one of the more realistic parts of the game too mind you, would be if:
*They have mommy issues/are genuine misogynists, like Synthetic Man, and have a mini-melty anytime a female character is on screen
*They don't play games and just look for reasons to bitch about them(ie culture warriors, on both sides of the aisle)
*They are tourists who have no clue about how MGS works and have somehow fooled themselves into thinking this franchises is in any way grounded in reality
And even then, the last one should make itself abundantly clear that MGS3 is not a game grounded in reality pretty early on. This only leaves people who are intentionally looking for things to get angry/outraged about, without caring if it actually makes sense for the source material(they only look at things in a vacuum, like I said before, zero context).
TLDR; MGS3 is one of the best games of all time, and if you are bitching about the "realism" of the game's intro then you got filtered out. Go back to playing shitty baby games like Coby or browsing /v/.