We were led to believe that many had their own views of what The Boss' ideals were (Zero and Co., Ocelot, Gene, and Big Boss, all had a different view of her ideals since all pretended to be successors to her, yet all ended up committing atrocities alien to her ideals). Also, MPO brought back the theme of "some men can't live without war" back. It was the whole Gray Fox scenario made more important; some people need war, they can't function in society, they can only live through war. This is also echoed by Big Boss at the end of the game, which he claims about himself.
Meanwhile, we know that Zero was behind the "Perfect Soldier" project. Considering Zero's taste for control, it sorts of became obvious that Zero would seek to establish an organization that would have to contain/control these "men who can't live without war". Big Boss was pretty much the proof of how dangerous they could be when he created Outer Heaven.
So we could see how Zero would seek to not only create an AI to carry on his will, because as The Boss said:
"Is there such thing as an absolute timeless enemy? There is no such thing and never has been. And the reason is that our enemies are human beings like us. They can only be our enemies in relative terms."
And this was very true by now to Zero's eyes; his organization was falling apart like The Philosophers before, another parallel, a theme that was supposed to be central to the game; according to Kojima MGS4's "theme" was sense: "how do we keep someone's sense digitally after they have passed way, how that sense is not the equivalent of will which is something that can't be preserved". Hence how a digital preservation of someone's sense could still end up leading to events that would have gone against that person's will, another parallel to what happened with The Boss' ideals after her death.
We also would come to understand how Zero would also need a system to keep "men of war" in control; enter SOP.
SOP was supposed to represent war made routine; Snake's hymn at the beginning of the game to how war has changed (too bad he only talks about smoking cigarettes for the rest of the game instead of continuing to speak as he did by the end of MGS2 and during that hymn to war) specifically mentions how war is now under complete control (yet not erased or prevented), and has become a mere routine (like a routine in a bigger system). War would be outright created by The Patriots because otherwise war would erupt randomly and dangerously, but it would be under control; the "men of war" would always have a place they belonged to, forever fighting but at the same time being kept under complete control.
A sort of "artificial" Outer Heaven.
This also tied in again to the idea of "sense" and the parallel to what happened with The Boss ideal's; The Boss' "hope to unite mankind" became Zero's will to control mankind future, and Big Boss' "hope to allow all men who could not live without war to have a place to call home" (which ties back to MPO and what Solidus clearly speaks of in MGS2 when it comes to be forbidden from passing over anything to the next generations) became Zero's will to control these men of war instead of giving them freedom.
It made sense, the whole series had been continuously shaped into that direction, and further so with each new game.
But I think somewhere down the line, the dead Zero and Big Boss and their "digitized sense" became the "living but very old Zero and healthy Big Boss and we have to come up with a way to explain that".
If Big Boss and Zero were dead, and if we had the ending were Snake died, only to be known as a madman to the rest of the world but having actually freed it, then maybe you can see how the past games seemed to have a very tight story that had been mostly about:
1- The Boss's theme: Since friends and foes change with the time, "because they are human", should the ideals behind leading humanity's progress be devoid of humanity so as to remain forever true, or should we simply accept our fates, loyal to the end, even if it means we may face each other in battle?
2- The Big Boss/theme: Since everyone should have a right to pass over to the next generation what they believe in; eliminating the freedom to war for humanity's progress would prevent a part of mankind to pass on to future generations what it can only pass through conflict.
Since the AI is modeled after Zero's vision of The Boss and Big Boss, a vision of respect no less but one that led to the opposite of what both would have desired in the end, it resulted in:
1- Humanity is united against its own will: Control of humanity through information and manipulation; forcefully uniting mankind, raising ally against foe when needed and uniting them under common causes when it benefits humanity's progress. The anti-thesis of what The Boss sought to accomplish, something much more reminiscent of what she described what The Philosophers had become (just like Gene's description of his "Army's Heaven" was outright rejected by Big Boss; the way he described it was no different than the way The Boss described what The Philosophers had become, again showing a parallel to how ventures to forcefully create an ideal world would always fail in the same manner, just like The Patriots later fail too).
2- The freedom to war is preserved, yet the war is devoid of freedom: The right to war, to seek revolution, to confront, is preserved within the system, except in reality all are fighting with "The Guns of The Patriots"; When the battlefield is under total control, war becomes routine. This, again, for the sake of humanity's progress.
"The Philosophers of today have no sense of good or evil. Their influence extends to countries and organizations involved in every aspect of every war. They have become war itself. That's how they operate. The sacrifices of war cause a shift in the times. This shift leads to renewed conflict and in turn triggers the next war. Like a nuclear chain reaction, each conflict sparks countless others, forming an endless spiral of war that will continue on for eternity. Do you understand what I'm saying, Snake? By consuming me and you the Philosophers intend to keep their cycle going forever."
And they did, ironically, under Zero's Patriots: through the preservation of The Boss' and Big Boss' ideals, albeit devoid of the original's will, it always leads to the same catastrophic results.
A lot of the recent developments in the story had been pointing at a more solid story, which I feel fell apart with the changes brought by the Big Boss ending. Big Boss did speak of the above, and his speech about how in the end he finally understood what The Boss meant, "let the world be" meaning don't try to change the world, simply live through it and endure, etc. But it was very messy, and a lot of the past games was glossed over and certain elements which had been hinted during the build up to MGS4 were never explored as a result.
The worst to me is how the line of repeated mistakes based on The Boss' will (Gene seeing himself as her successor ends up trying to create something akin to The Philosophers he hated, same thing with Big Boss and his Outer Heaven, same thing with Liquid and his own Outer Haven, and in a way possibly similarly so with Ocelot considering how he says in MPO he wants to make the world The Boss (his mother no less) envisioned a reality) suddenly was no longer relevant; Liquid Ocelot was not the result of two individuals seeking to fulfill the wills of The Boss and Big Boss through, fatefully, one individual, but just Ocelot's plan to revive Big Boss and have Zero and his Patriots organization killed. Disappointing and I can't believe it was the original intention considering all the above.
I think they scrapped a good chunk of what was originally supposed to be more about the "sense" theme which Kojima said was to MGS4 what genes were to MGS1, meme to MGS2, scene to MGS3, and specifically said that it was supposed to be about "digitally preserving someone's sense after they have passed away", and I also think that Snake dying at the end was as such supposed to have different repercussions on the rest of the game and more specifically how the story would be told.
The new questions that resulted from the sudden introduction of a "Snatcher Project" in the MGS world were unnecessary to me.