I think something happened during that 40 hour Konami Bootcamp, as (correct me if I'm wrong) all reviews were outlandishly positive, yet there isn't a single fan who is totally content with the game.
There's no way the mission design and story that we got was the grand plan all along, but instead of wishful thinking of getting those cut content, why not focus on why the final product failed so spectacularly.
Like I said before, there are plenty of movies with essential content cut or grueling troubled productions. Take the original Robocop or Predator as a minor example. Those two movies were a genuine nightmare to make, things got so bad that the cast of both movies were trying to kill each other on a daily basis. Did it affected the final product? Not under a skilled director.