This is due warning: this thread is for people who have either finished the game or spoiled themselves beyond saving. If you want to keep your mind untainted, go no further.
As people dig through the files we are finding more and more cut content from the game, including what appears to be the title screen for an entire third chapter. I'll post the pictures below and link to the thread where they can be found:
In addition to this we also know that Kiefer had many lines cut:
Including one important post-game monologue: https://a.pomf.cat/abcyrl.mp4
There's also the cut Liquid Snake mission that's been going around:
This is what we know of so far, and we will undoubtedly get more. Cuts are standard, and I'm actually in a camp to believe that Keifers lines were intentionally cut so that Snake could work better as a self-insert. But stuff like old Snake and that chapter 3 heading send some bad messages. I wonder how much the Kojima-Konami meltdown affected this game's development; I wonder how much this game's development affected the Kojima-Konami meltdown.
I always found the game's structure odd. For one, MGS4 and PW both have 5 chapters and an epilogue. This has two chapters, which is a non-standard set-up for any medium. Chapter 2 mostly being a retread of chapter 1 also raises questions about cuts. I think its undeniable that the game we got was fantastic, but I wonder if Kojima and his team were faced with a time crunch by Konami and had to either sacrifice narrative or sacrifice gameplay quality and went for gameplay.
We will probably never know what this game was supposed to be, but I hope one day they release a "grand gameplan" for it like they did for MGS2 (which is a really interesting read btw if you're a fan of the series, it's basically the outline of MGS2 before it went through radical changes to become its current form: http://junkerhq.net/MGS2gameplan.pdf)
It's also true that Kojima wanted to structure this game more like a television show. I wonder if future chapters will come out as DLC and act like "seasons". Either way, it's a little fishy/sad to see and wonder about all that is gone.