I for one don't think the continuation rule is that big of deal. I've heard people bitch about bracket resetting too, so you will never make everyone happy with how you run the tourney.
I also think it's stupid that everyone is bitching about the continuation rule, but no one is applauding how MLG does their matches first to 3, when at normal touney's it's best of 2 of 3. Why has no one mentioned this? I love that MLG does first to 3 because it gives people more chances to come back if they happen to just blow it 2 matches, and can come back in the 3rd, much more hype.
I'm not saying the continuation rule is the BEST, but it's definitely not all hell breaking loose. Certain scenario's people would favor it, and certain ones people will hate it. Can't please everyone, and beggars can't be choosers.