i personally think everything was tied up quite nicely, i mean, we find out what happens to raiden (the abomination that he was in the first place to the series) and of course, he was one of the smallest portions of the entire
MGS series. Of course, there are enough conspiracy theories in there to make even the harest conspiracy theorists' head blow up... gotta love it
and my favorite part of the game has to either be fighting Psycho Mantis, or the Metal Gear battle, when you pilot Rex vs. Ray