I didn't know there was so much hate for the mgs story line. I always liked its over the top nature and lengthily cut scenes. I guess the game is compared to a anime in terms of how its delivered. I think a lot of people hate the cut scenes and odd writing is because they are used to other styles of writing and story telling. When you look at the gaming industry stories belonged in rpg games mostly and games that had anything to do with a gun had a basic story framework that pushed the player through missions etc. So people who play mgs for the stealth action it provides they also expect it to be a little shallow on the story side because all they care about is the next checkpoint. People who are fans of kojima's work are living in the moment and taking in every tidbit of information and story development. I will agree that he may need to explore other ways of getting information across without huge cut scenes but give the guy a brake.
