My suggestion is only the top two entries from each region move to the big show. (I'd actually suggest it be only one, but the natives might go crazy.) The problem as I see it is from each region you get one good to great entry, a lesser and a lesser. So one worth making the trip and two which really should have stayed back on the bench. I judged two flights of 11 and had 3 in one flight worthy of advancing to a mini-BOS and only 2 in the other worthy of advancing to a mini-BOS.
Alternatively, implement a minimum score needed to advance to the final round. - But honestly, that's probably a small part of the problem. I think past winners should automatically get to enter as many beers as they want the next year. This will ensure high quality entries from the best brewers. All other slots should be assigned by lottery to keep the open feel.