@DeadNotSleeping: It actually was a fair comparision, since the storytelling is what matters. If the game has good storytelling (with good gameplay), it's praised like OOT, but bad storytelling leads us to MGS.
The games are supposed to tell their stories by their own merits, as integrated to gameplay. More storyheavy game with more CGI leading the story, the more it alienates from being a game. "The time and era of this story is unknown..." is enough story for a game, which actual gameplay is alienated from the storyplay. If you can't add the story into the gameplay or run the story in-game, it's better not to have one. For example Metroid had a great story.

You didn't tell me any reason why Mario games would need a story? Why would Mario wonder that? After all, Mario is a fictional character who can't think of his own. And even if there would be a story that answers your questions, what would it add to the game? What if Tetris would be about bald space marines? What would that add to the game?

Why couldn't Metal Gears focus on finding and destroying Metal Gear? Or to be more specific, why couldn't the story be told during the gameplay?

Is it truly a double standard, or merely an acknowledgment that story is only one way to make a game entertaining, and that other ways -such as the ways Nintendo typically takes- exist?

dunno. To me, the Zelda stories are the most immersive Ive ever seen in a game.

Of course, depends on the genre. I dont expect ANY story ina FPS, in fact if it gets too story driven, it turns me off. I prefer shoot now, ask questions later. Probably why Timesplitters 2 will always be one my of my favorite games.

I couldn't disagree more.  I think that the amount of story in Metroid is just perfect for the type of game it is because it gives you exactly as much story as you want to see (because you scan as much as you want).  People who just want to run through and look at the pretty environments and kill the bad guys never get stopped dead by half an hour of explanation they don't want to hear.  The scanning is not what I would call super hard to do, so I'm not sure why it has to be more "accessible" for those who want more. 

As for Mario, you still seem to just be assuming that it would be better with more story without explaining why.  Some games (in my opinion and obviously that of many others) just don't need much story, and not just games like Tetris.  I'm playing Contra 4, that doesn't have much story.  Someone mentioned Mega Man 9.  These games aren't bashed for not having a good story because they don't have a need for one in the game structure.  Some novels don't have or need romantic subplots. 

Some games are hurt by lack of story.  Some are not.  Mario belongs in the latter category.

OP: Here I'll tell them to make all there games into books.

@bdbdbd Funny thing is I have the book right in front of me today and when I wrote that. ^_^