I have a few theories about the unfinished nature of this game.
There are rumors that a third open world environment was cut, and I recall multiple sources stating that there would be several locations to visit in game, implying more than just two. There's the island Eli escapes to in the cut episode 51, which we know for a fact was into development enough to have cutscenes taking place there. My guess is that the "repeat" missions in Chapter 2 were originally supposed to be new missions at Eli's Lord of the Flies homage, culminating in a final showdown with Sahelanthropus driven by young Mantis and Eli. This would have led to a different ending and ended Eli's and Mantis' plot threads.
My second theory is something I think probably changed as the game was being made, rather than being cut at the end. We begin with a flash forward to Outer Heaven, and all of the trailers point to this being Big Boss' fall from grace. I don't think the Eli story was meant to be the end - I believe we were originally supposed to either retake control of BB himself after a timeskip, or complete more missions with Venom leading up to the Outer Heaven uprising. Part of my reason for suspecting this is not only the marketing for the game and the fact that Venom is there in OH at the beginning and the end of the game, but in that in one of the very first trailers, we see one of the very last cutscenes in the game, which is Big Boss on his motorcycle. That entire scene seemed to be leading up to something else.
The chapter system makes no sense because there are only two chapters. I think Kojima originally truly intended to fill the gap between Peace Walker and MG1 with multiple chapters, perhaps 3 or even 4 or 5 of them, but the sheer expense of the game made him fall short of his vision, so he was forced to compromise. I also bet that Konami was very upset with where he wanted to go, how much he had spent on just the first chapter or so of the game, and how much left he still wanted to do. He also made decisions like creating a brand new engine, hiring high profile Hollywood actors for mocap and VA, which likely cut into the budget a LOT. Then they realized he was going to do another project, also likely of a huge budget, with P.T., and they got scared and pulled the plug, causing the game to be rushed to shelves and left largely incomplete.
I feel like Kojima's vision for this game was insane. In a good way. Too insane to be fully realized, to the point where it got cut down both during conception (possibly several times) and then again towards the end of its development. These are just my own theories, and I have nothing to back them up other than what I've said, but I feel like something went down during development because the marketing for this game and the finished product don't seem to agree with one another.
