I think a reasonable case could be made that Champaign Illinois (which hosts UIUC) is more of an urban area than those two cities. At the very least, I think it's better than San Mateo.
I agree that San Francisco sucks (and I lived in SOMA and in Noe Valley, both of which have relatively good [for the area] transit), but it is at least an actual city.
The obvious elephant in the room here is San Jose, and it's telling that you didn't mention it, opting instead to pretend that San Mateo was a "dense urban area". San Jose is an urban center. But it's miserable; nobody talks about moving there. The fact is that San Mateo sounds plausible because of its proximity to San Francisco.
† For Palo Alto, I mean University; you don't need to point out that El Camino runs through it, I know where to go to find the strip malls. :)