For example, the latest data shows the Los Angeles metropolitan area as the second largest in the country, with a population estimate of nearly 13 million on July 1, 2008. Unfortunately, the intrinsically tied Riverside-San Bernardino-Ontario, CA metropolitan area is no longer included with Los Angeles which is listed separately as #18 on the most populous list with a population of 4.1 million. Likewise, the #17 San Francisco metropolitan area no longer includes the adjacent and interconnected San Jose, with a city population of nearly a million.
With the division of metropolitan areas into their components, it's a challenge to compare true population regions. What are your thoughts and/or do you have suggestions for solutions?

Comments
The rules for defining, or delineating, metro areas are now up for review in a federal register notice. Email me if you want the link. This is the time to comment “officially” on this issue to the people with the power to change the rules. One of the issues is how “combined metro areas” are established, which is the very issue you refer to re San Bernadino and San Jose.
With the emergence of Silicon Valley (San Jose) as the preeminent area driving the economics of the San Francisco Bay area, it seems the city of San Francisco might be considered part of the metro area of San Jose?