Art is up to taste, so as a critic it's easier to recognize something as art that maybe you don't partake or enjoy, like post-modern literature, Jackson Pollock paintings, or anti-art, than to fail to recognize it at all. That is what makes Roger Ebert's argument weak.
The best example of sublime art in a game would be Myst. Outside of that minor examples might be The Stanley Parable, Half-Life 2, or Façade.
If there are a few examples of video games as sublime art, then I think that establishes the medium as art. The movie Doom is abysmal, and yet the late Roger Ebert would put that on a higher plane than these great examples? That seems irrational.
I think the greatest issue is with the video game work that Roger Ebert was exposed to. If you had never listened to music in your life and only read books and seen paintings, and then you were introduced to pop radio or a host of folk death metal albums, you might have the same reaction as he had had to video games: seeing that music is an inferior form, merely an amusement rather than art, instead of seeing that certain genres are more crude than the level of sophistication enjoyed in his books or paintings. Being surrounded by the most popular or violent collections of medium aren't encouraging in the way that seeing an instance of sublime art would be.
The examples that Kellee Santiago gave were really independent renaissance games, which are often minimalistic or contain subtle elements. Instead of an example of an epic like the Iliad or Lawrence of Arabia, they are a short story, of any quality.
And just as Roger Ebert did not live in a vacuum and had certainly seen video games played in movies, he has obviously seen them develop from the very beginning. The examples of early arcade games are like simple drum signals compared to a symphony. It might be that he just missed out on what might have been a great artistic experience.