Necessity is the mother of invention. Perhaps some good suggestions will rise out of the chaos that was this years registration. I'll throw some random ideas into the pot.
I think the obvious issue is growth and demand. While the AHA has taken steps to manage growth, the growth in popularity has been explosive. I think the key is in finding ways to increase capacity. In Seattle they are getting ready to host the Comicon comic convention, and expect over 50,000 attendees over 3 days. So that tells us that convention centers can handle much larger crowds then the Homebrewers conference currently draws. I'll give you all of the 50,000+ are likely not staying in hotels for the entire conference, but I bet many are.
for the NHC the coastal regions max out quickly, as that is where the people are. Perhaps first round can be done in more than one event in the more populated regions. Instead of doing 750 entries in April, maybe you do a 500-600 entry first round in March, and another one 4 weeks later. You get to double up on the entries. You leave the total entries per brewer capped at whatever 15 entries, or maybe 10. This would also likely make the final round at the NHC a two day judging event. Maybe you can bump the registration to $15 or $20 per entry to allow some nicer incentives to bring in more judges. Maybe offer a separate judges banquet or something like that.
Maybe you run an east and west coast regional conference before the main conference to slim the entries down to the main NHC. Until there is are some significant increases to capaity, it will be difficult to alleviate the pressures currently being experienced.