You know, I looked back on a few MGS games and scenes and here is something I felt off about them
MGS 4 - Am I the only one disappointed we never had the Patriots' AIs talking like in 2? They did show to be frighteningly smart and very controlling. You would think that a scene or two with an "avatar" of the AIs appearing to talk with some of the characters, maybe Snake or Liquid Ocelot, perhaps to try to convince them why its preservation is the most beneficial outcome for humanity and that humanity CANNOT exist without them long term...that all the tech, nano machines and etc will not simply balance itself out. Without their control, they will only get more and more powerful until humanity figures a way to eliminate itself. Yeah, this could all sort of foreshadow MGR and its borderline cartoonishly OP nanomachines (lets not be naive and think that the nanomachines the Desperados used have died with them), imagine if Armstrong's nanomachines fell into (more) wrong hands? Raiden cant exactly kill an entire army of nanomachine supermen, he is still one cyborg at the end of the day. The Patriots most likely knew this outcome with nanomachines bringing forward walking Weapons of Mass Destruction and knew that their control, while morally evil, was the most beneficial outcome for humanity. Besides, I even imagined one of the AIs mocking Snake's decaying mortality by saying that they will be immortal and ever lasting while he will only have a year at best to live, to which Snake just gives them his equivalent of "Fuck you" cleverly while not letting that get in his way.
The patriots's AI felt scary in 2, in 4 they are pretty much non existant.
MGS 5 - The scene where they say Liquid isnt Venom's son always bothered me, are we ignoring that they outright told the twist right there? You can say its foreshadowing but I disagree, anyone who knows MGS can tell what this means. What? Are they seriously saying Liquid suddenly ISNT Big Boss's son at all? That he never had any connection to Big Boss and that maybe his entire backstory was a lie told him? Or the most likely scenario that we arent playing as the real big boss at all? Which of these fucks up the lore the least? The only other possibility is that it was a lie or botched result (which could work but clearly they werent building towards that). I have a lot of problems with MGS 5's story (I honestly think MGS 5 went for a "gameplay over story" approach like MGR) but this was one of the scenes that made me wonder what was Kojima thinking...he just spoiled his own twist right there!
My unpopular MGS opinion: I don't like The Boss. She's basically the patron saint of "just following orders." She continues to follow her superiors even after they repeatedly betray her. Loyalty is one thing, but when her superiors have no loyalty in return it just makes her look like an exceptionally talented useful idiot.
One of the cornerstones of her ideology is that "enemies change with the times." This is treated by the other characters as some incredibly deep insight when it's patently obvious to anyone with a basic grasp on human history. The other point of her massive infodump at the end of MGS3 was a tract on globalism. I'm not going to comment on that one way or the other but why do Japanese developers always feel the need to push the "no borders" angle? They live in the second most ethnically homogeneous nations on Earth and treat foreigners like shit. I'll listen to their thoughts on globalism when they have experienced it.
I could stomach all this but her life and motives served as the driving force for every influential figure for the next forty years. A huge cold war between Zero and Big Boss that is party responsible for a massive surveillance state and the war economy came about entirely because they interpreted her will in different ways. They then spent the rest of the series lecturing the player about how Christ-like she was.
TL: DR The Boss is a hopelessly naive useful idiot.
To be honest, what you are doing is an "interpretation" of her will. MGS4 did conclude her true Will was to let the world be. What she wanted was for the world to just get along and yet maintain their indepedency. The "no borders" wasnt for globalism necessarily, it was just for the world to come together and not focus on supremacy but rather being capable of laying down their weapons for a better world when there is no need for fighting.
It was perhaps too idealistic to ever come true and maybe thats the whole point, both Big Boss and Zero tried to do their own version of this "perfect" world and both versions did come true in the worst way possible. The Boss was a good person that had her entire life controlled, her wishing a world without "control" was expected of her.
What she wanted was for the Cold War to end and people to just stop needless violence, she had lived this her entire life...however I doubt she wanted needless control and violence to achieve this ideal world (which are the methods Big Boss and Zero used). In the end, Solid Snake was the true carrier of her will, he wanted to create a free world without weapons of mass destruction, where people could decide for themselves but be ready to defend themselves and others, simply for it being the correct thing.