By making the shipping options cater to the lowest common denominator, it has seriously hosed up those of us that use UPS, FedEx, or USPS plugins. Now my customers are offered the most expensive shipping rate by default (and I'm getting annoyed calls) and there is no way for us to now reorder the shipping methods.

Either they didn't think this one through, or they haven't provided the proper training for the rest of us that don't use one fixed priced shipping method for every product like Woocommerce assumes.