Kojima horribly mismanaged the project.
That's what it comes down to. He couldn't keep it on track, and so we got a disjointed mess sans an ending.
This is not unique to Kojima. Who is not mismanaged a game project? Almost all AAA game project is either have cut content, horrible before patch, or missing deadline and must be postponed lately.
Even the Star Citizen is turning to kickstater mostly because Chris Robert cannot agree to a set deadine before doing the project.