I don't really agree. First, having lived in a few of those "megaregions", I really agree with the author that they each have distinct and unique characters. I also see other nitpicks in some comments here about "there is a lot of wide-open spaces in those circles!" - that seems a bit silly to me given that many of those circles include wide expanses of ocean, and it seems clear to me that the author just means to highlight the related urban areas, not the emptiness in between.
But more to your point, there are plenty of other sizable cities that are not part of the megaregions the author highlights, and I would agree that those cities are less dynamic and less engines of economic growth due to their isolation - places like Phoenix, Salt Lake City, Minneapolis, etc. The only difference I think is that it "feels" to me like there is an emerging megaregion on the eastern slope of the Front Range in Colorado, i.e. Ft. Collins-Boulder-Denver-Colorado Springs area.