Spec Ops is the finest to come out recently, imo. I think the problem stems from the attention things like Mass Effect and GTA get. When GTA4 came out, people were actually comparing it to the Godfather, and it's really nothing close. Both are fun and interesting, but their plots are extremely formulaic and the dialogue is about the quality of a B or C movie. But they get a lot of hype, so people outside of gaming find out more about them and see that the story/depth really isn't all that stellar - about what you'd find in those trashy novels at the airport.I think there can be art in a game, but the game itself is usually not art. There are a few examples of games that attempt to be art. I think Braid is one of the very few that succeeded in being both a game and an artwork. I can't think of any others at the moment. Guild Wars 2 has a lot of great art and an artistic style that I really enjoy, but the game itself isn't art.
Spec Ops steps outside that because immediately you can't take the story at face value. Some people don't like what they think it tries to do, but everyone has a different interpretation on what it's actually doing and why it's doing it. The head writer admits that there are things designed to bother and upset some people about both the game design and the story, and I'm pretty sure most people who finish it do so inspite of not having fun, in a way like watching Schindler's List. It's not meant to lead you from A to B, it's meant to inspire a reaction, which I think great art should do. It does contain formulaic devices, but for the express purpose of showing how formulaic and contrived they actually are.
As for the article, he's writing in response to the MoMa exhibit that features a bunch of classic games. As I said before, I think great art should be to inspire a reaction and not simply lead you from A to B, and in that sense I agree with him about a lot of the games chosen. That said, not all art works that way and especially in painting and sculpture, a lot of things are just meant to be aesthetically pleasing rather than thought provoking.