Just got an email back from the Pokemon Company. Here is what they said.
"Thank you for your interest in Play Pokemon events! We encourage people to get involved, and express their opinions to make our programs better for everyone. In regards to your selected topic of Video Game Championships elimination methods, we completely agree with your reasons and motives. We will do the best we can to make swiss parings standard for regional play. Thank you for you suggestions and please continue to enjoy Play Pokemon.
Sincerely, The Pokemon Company International"
so don't know if what they are saying is BS or not, but if they really mean what they say, hopefully we will never see Single Elimination again at regular regionals.