There is a theory that the game was unfinished thanks to Kojima's outing. Given the nature of his departure and the drop off of quality in the game, recognized by most players, its very likely it affected the game. Most people would assume, Konami, like any other reasonable company would wait till the game was finished to remove him, but as we have all seen Konami is not very reasonable. Add that MGS:TPP and MGS:GZ where so close together release wise, and you have even more compelling evidence it was unfinished.
Another theory is that Konami took out stuff from the game to turn into DLC, they can't really make DLC with Kojima gone after all. These are just theories, but it wouldn't be that surprising.
In this day and age, with the Internet, ignorance is a choice! And they're still choosing Ignorance! - Dr. Filthy Frank
