I think you can make an argument some of this stuff rises to the level of a decent-ish sci-fi novella or so. It pokes you in the eye because the medium is typically so narratively impoverished. But both of these, like many genuinely emotionally engaging games before them will be well-forgotten in a decade or so. The Discobolus, Hamlet or Guernica this is not.
You have to keep in mind that gaming is a very new medium. The more artistic variety of games has only been around for a few years. To demand something on the level of Shakespeare is very disingenuous.
A better way of seeing why games can be art is through a comparison to movies. Games can be made to essentially be movies but with the crucial difference of immersing the viewer entirely into the world through the choices it presents.
I do not see how adding more possibilities to an existing art form (movies) can ever demote something from art to non art (whatever you think these things mean).
I think a game like last of us is a great exploration of the potential of this form of game play.
Again, this is non-responsive to Brian Moriarty's and Ebert's argument. They specifically address your points and all you have is 'I don't see how'. And do you really think anyone is going to give a hoot about 'The Last of Us' in 20 years? 'The Third Man' is about to turn 70.
Perhaps also To The Moon, by Freebird Games.