I don't like the idea of limiting based on entry fee - People are currently excluded basically because of luck - which is wrong. But, I don't think that exclusion based on your financial situation is good either. I think if you are going to exclude people (which is basically a necessity) it is better to do it based on quality of beer brewed. Not saying there are not problems with that as well (you pointed some out) - but at least is is something that is a fair way of excluding. In this day and age of technology, keeping track of who earned "top 3 finishes" in 20 competitions across the country would not be very hard at all...... I would go so far as to say it would (apparently) be easier than having 10,000 people register for a competition at the exact same moment.
If this method were used, then yes - you would have to enter in the category you qualified in. Would not necessarily be the same batch of beer..... but then again, neither is the second round. Plus, if you knew in advance that you had a particular style qualified, you could plan your brewing to certain beers, instead of "sending what you have on hand." I don't think the NHC should really be a competition that people use "to get some feedback" - there are hundreds of competitions for that.
Your ability to enter should not depend on luck, $$, internet connection or timing - it should simply depend on your ability to brew good beer. My guess is that the Kansas City regional will be judged largely by the KCBM contest judges, the Milwaukee one will be judged by lots of the same that did Midwinter, and St. Paul will have many of the judges from Upper Mississippi Mashout...... and so on and so on...... there are 20 competitions that could be used for "top 3" entries IF that were ever an option to pursue. Not saying it is the right or best answer.... but it is feasible, and it does have some merit to it.