I wouldn't be surprised if they quit doing commentary on every episode pretty soon. Maybe not on the next set, but in the next couple.
With the show quality being what it is, and the "who cares about the fans" attitude many of the staffers during these seasons had.. I'll be surprised to see commentary on every single episode from this point on.
But, that's just a guess.. I'm surprised they bothered to continue it through the Scully years. So, I guess it wouldn't be a shock either way.