I am a huge fan and supporter of USAC And the Cat 1-4 system. But the National ranking system for Cyclocross and Mountain biking is horrible. In additon, if promoters don't submit their results, it gets worse. But it does not seem that USAC mandates this to the promoters. Which makes me think that if USAC is granting the license to the promoters, that they would at least want the results in return to make the USAC rankings more ligit.
As for crossresults.com -- Simply awesome. Not only is the ranking system more accurate, but there are some really cool tools, data, charts, and graphs to help you monitor your progress. Such tools as "Head to Head" compition tracking which makes racing againist your closest rivials more fun even if its for battling out last place every race is one of my favorites! But on a down side, the promoters all need to use the same computer software so crossresults.com can get the data onto their site. This is a problem with our local race series currently.
As for a fix. My 2 cents. Cat 1 racers race Cat 1 racers. Cat 2 racers race Cat 2 racers Cat 3 racers race Cat 3.... etc. But then you run into problems with age groups or "Masters" Cats. I'm not sure there is an entire solution to the issue, but streamlining some of the Cats / classes and having USAC standardize the race classes across the country for every National / local series may be somewhere to start.