The problem with comparing the regionals/nationals relationship to other tournaments is that they vary so much in size in and skill level. Even states has to much variation to be counted for byes in my opinion. Winning BR's, and cities is definitely an achievement, but it's just not a comparison to the skill level that's brought to regionals, especially with the upcoming change in schedule.
Keep in mind, the other player is also only playing 2 more rounds than the regionals winner. The regionals winner played an extra 13 to get those byes. If the 6-3 random player couldn't make regionals, then that's unfortunate, but Pokemon is a game that favors people who can attend more events (and I don't have a problem with that). I understand where you're coming from, but I think Pokemon wants to encourage more regional winners to be in top cut.
Think about it, the minute you win a regionals you can be considered a big player. Maybe not the best in the world, but at the very least above average. There's only a few of you every year, and you definitely do show up at nats as one of the people to beat. For that reason alone I think the byes are fine. Probably not for 2nd place even, and definitely not for states, but the winners should have an advantage over nationals. They already proved they have what it takes to be top cut material at nats, as for everyone else we have to prove it.
The other thing too, is that once you go 6-3 you're putting your chance of getting into top cut up in the air. I understand anyone can have a bad day, a bad match-up, or just get unlucky, but ultimately when you show up at a nationals you need to go in the attitude that you're 7-2 or missing cut. I know this may seem kind of harsh, and I'm not saying going 6-3 means you are a bad player, or anything of the like, but once you're 6-3 a good portion of the odds are based on luck (even a great player can lose to someone like Pooka on round 1).
Finally, once the regional winners make it to top cut, it's top 128. At US nats, even just making top cut is tough, but if they really aren't good they won't go very deep. I know this isn't going to be much consolation to those who don't make cut, but I feel like those who have proven themselves deserve a shot at top cut. With regionals not providing anything other than rating points when looking towards worlds, I really feel like this is the best way to push a regional winner towards that world invite, which is ultimately what you're after. So giving them a bit of a bump to top cut, is simply pokemon's way of saying "you won regionals, you deserve a better shot at making it to worlds." For that reason alone, I don't really see any problems with handing out a double bye to the winner of each regionals. (If it's only to the winner do you know how few people that's going to be anyways?)