Hopefully nobody here will tell you to get a life. We're on a site called Hacker News, discussing artistic merit in video games. So it's good.
I have a different view of art than you do. I don't think that art must necessarily illustrate the human condition. Do Bach's cello suites make any sort of commentary whatsoever? Not to the untrained eye. They're just expertly crafted pieces of music. That, to me, is the core of art: not necessarily a statement about humanity but the practice of honing your ability with a craft. You can have the best idea imaginable but if you can't tell it well then it's not art.
I'm certain that BioShock DOES mean to do what you think it does. It absolutely attempts those route literary devices and it does a pretty good job of that. However, I would not for an instant call BioShock art, because it is not a movie. Its purpose is not primarily to tell a story. Its main role is to be a good game. And at that, it fails. It's fairly monotonous and while it has great ambience, the gameplay doesn't distinguish itself much. The story doesn't tell itself WELL. There were a few interesting moments from what I've played but that was it.
In my mind, the primary method of art in a game is that of the game itself. The best artists are the ones making the most fun games. That doesn't necessarily mean greater themes: Zelda is very black-and-white, for instance, in terms of story. However, a game doesn't require a story if it does its job well. Zelda doesn't, and yet THAT is what I consider to be the highest art. It's a beautiful, memorable game.
Portal? That's as close to sublime as you get. It DOES have a story, and it has a good one. And no, it doesn't have themes, any more than A Midsummer Night's Dream does. Which is to say, you can see themes in it, because they're there in both of them, but the main thing about each one is that they're enjoyable without focusing on the themes. Shakespeare isn't great because he told themes: he's great because every line he wrote was beautiful and absolutely fit whatever he was writing. The components have to fit together. That's what makes a good game.
Half-Life 2 has a story, and it tells the story well. The story is incredibly well-written, too, and it's told in the game brilliantly. The gameplay is surprisingly emotional: you get very involved in the gunfighting because of how slowly it develops. You feel extremely in the game. That's art. That's what gaming is all about.
Final Fantasy? It always tries to tell a story. And the stories are usually very thematic. I think it's slightly going downhill, but the one I mentioned (II/IV) was sublime. The graphics, music, gameplay was all very simple, but it was beautiful. It was evocative. The soundtrack in particular is stunning. The story was not particularly complex, but it was emotional and told itself well. That's art at its best. When I played it at 8 or 9, it changed my life. It made me want to become a game designer.
You're in the mindset that all mechanics have been done, and so art is just doing an old thing in a new way. That's silly! We're at the phase in video games where NOTHING has been done. We're like cinematographers in the 20s. We can do ANYTHING and it's new, and so we don't have to worry about exhausting old ground. Portal is art because it created a new game mechanic! It's something that was never done before. And not only does it MAKE the mechanic, but it polishes it considerably. It's tight, it's exciting for the entire game, and it's new. Art.
And Nintendo? They're making the greatest art of them ALL. I look at them like I look at the early silent films: they don't use an involved story, because they're busy focusing on technique, style. Every Mario game adds new ideas. It keeps on redefining the platform genre, adding new things to do. That's art. Nintendo takes the craft that Miyamoto started as a boy and continues to refine and perfect it. It's why I'd argue that of my favorite games, Nintendo's made about half. A handful of Zeldas, a few Marios, even Animal Crossing, Wii Sports, and every Super Smash Bros. They're not "literary" but they don't have to be. They don't need symbols. They're all about incredibly fun and radical new game ideas, and they're all the highest form of art.
tl;dr - BioShock's story isn't good enough to be considered literature, and it has mediocre gameplay. I think art means making fun games above everything, and BioShock is a big fail for that, even if it is pretty.