Regionals has nothing to do with the "best beating the best". It is about finishing within the top 12 in your region. And of course what if the top 24 are all located in say the East Region? In that case, 12 of the "best" get left out, but 12 undeserving runners from the West competing in the championships. Unlikely, but this points out the complete fallacy of the two Regionals setup.
What if the top 24 800 meter runners in the country came from UCLA, Stanford, Oregon, USC (the big time programs etc. in the Pac 10). In that case, 12 of the "Best" would never get chance to go to Nationals, because 12 "Lesser" runners from the East would qualify.