The NFL has the same problem. I'm kind of torn on the reseeding idea in any sport. I kind of like it for things like football playoffs, but not for something like the NCAA Tournament (like in the Sweet 16). Not sure why I like one over the other? Just do!
I prefer the brackets stay complete once built. Dont penalize a lower seed by always making them play the hardest team. Just means the seeding wasnt that accurate
Doing it the way it is almost always ensures that the best teams make it to the championship and that therefore the championship is a really good game.