Xenogears: people will often mention this game on lists like these but most of them are quick to dismiss the second disc and treat it like crap. It's one of the most well written stories for a game, actually, one of the most well written stories: period. Anything really wrong with it, as far as writing goes, is mostly due to the medium [video game] and the translation/coding. As for the story itself, it is quite the epic tale: had it come out at just the right time and in the right format, it could be a "LOTR" or "Star Wars" type phenomenon. It sadly lives in Evangelion's shadow but it is SO much MORE than Evangelion, and I just wish it was appreciated for what it is. Xenogears is not only an epic tale of war, mystery, religion, and intrigue, but it is a beautiful love story and coming of age piece.
Xenosaga is close, but it's not finished yet, and it seems it never will be finished. However, the only thing that brings down the Xenosaga is that Shion never comes full circle like Fei does. With Fei, he's a whiny arrogant self absorbed cowardly asshole, but in the end he becomes noble, strong, courageous, and fully realized of himself and what truly matters. With Shion? She is such a
ing bitch in episode 3 and doesn't deserve to live. But it's still a beautiful story, with great characters, wonderful setting, and so much background and lore that you'll never be done with it.
Both stories are very text/dialog heavy, but if people let MGS do it, then Xenosaga should get the same right. I don't see why MGS has to be so..drawn out..long..and over written..when the story doesn't even begin to touch even a bit of the subject matter any Xeno-story does. With the Xeno series, you actually want to listen to the dialog and read the text...while with MGS it's just like "OH GOD, GET THIS OVER WITH, NONE OF THIS MAKES ANY SENSE, JUST LET ME CRACK SOME NECKS ALREADY"
As for shorter self contained stories: how about Parasite Eve? A short 20 hour game with a non stop story full of great suspense, horror, and sci fi themes.