Personally, I think the answer is to remove first round byes altogether. And I'm saying this as a Regional Champion, who has a Bye card that I could take with me to GenCon this summer.
I agree with this 100 percent. As a regional winner, if they announced that they were removing all first round byes for Gencon, I would be much more happy than annoyed. The first round bye creates significant problems in tourney structure. I believe it should go away.
However, I also feel that in it's place there should be an extra kicker for winning a regional, national, or continental level event. This is only my two cents, but I would like a Tournament of Champions style event at Worlds. You need one of those fancy cards to get into the tournament. This would in no way replace/overshadow the World Championship Tournament, and would be a much smaller/shorter event. I think I would enjoy an invitational event in a tournament structure where registration in mostly open.