The problem with the whole "best story" argument is there are two ways to judge a game for that:
1) The depth of the story. In other words how well the story would compare to a good book.
2) Story integration. In other words, how well the story is told along with the gameplay.
Quite often they are mutually exclusive. Many adventure games tell a story that follows #2 very well, but is a simple story and therefore fails #1. Some JRPG's try to make a very detailed and in depth story, so it passes #1, but sacrifices game quality by making you sit around and watch what is essentially a movie, so it fails #2.
In my opinion, if you want good story, go buy a book. No matter how hard game designers/writers try, they cannot compete with a good book on story.
