Yeah, that's what I've been saying. Games have been trying to follow movies' lead when they should be trailblazing their own. The whole 'external story' is one such way of telling a story that is only available to games. Every time someone watches a movie, reads a book etc., they're looking at the same story. But every time a gamer plays a game, the experience is different. Especially if it's something like Dwarf Fortress, in which a buttload of random stuff come together at different times to make each experience truly unique. Then you tell your experience to other people and they will maybe draw your characters, or maybe build giant statues [http://dwarffortresswiki.net/index.php/Cacame_Awemedinade] of them. A similar thing happens with any online game, although I think such an experience is collective and can only be truly meaningful if you are in the same couch/househould/lan house/etc., you know, if at least all of the involved would need to use the same toilet if necessary.
But I don't think external stories are the only way. Internal stories can also be refined, lose some of the strict directing of linear storytelling, and focus on evoking feelings rather than telling tales. I do agree that Bioshock style stories will, in the future, become, if not rarer, at least less relevant.
I would also like to add that, when Yahtzee said that making a game have pretty cutscenes to make it more like a movie is like making a movie having words show up on a blank background to make it more like a book, his analogy actually fall short. Gamers sometimes say that games are the next step after movies, but they are not. Games are interactive media, movies aren't. Movies are on the same branch as books, TV series, radio plays, etc. Games are on the same as RPGs, board games and improv. They are media that changes depending on who is performing and/or acting it, and thus should aim to provide a broader experience, because the narrow ones will not survive the transition. (Theatre is kind of between the two; a play can be the same every time it's performed, or it may allow improvisation so that it differs. If it breaks the fourth wall, all bets are off.) To expect all games to tell a story the way movies do is like expecting to have to draw a card explaining what happens to the poor man in the giant shoe after every round of Monopoly.