BWSS has a pretty good reputation. I have talked to a couple of people that have taken the class you are thinking of and their experience was similar to what you have heard herr already.
Bottom line, and course, sailing or otherwise, depends on the instructor. They usually put their better instructors on the longer courses because they want to keep them paid, happy, and returning. The newbie instructors usually end up with the short courses.
I did charter a boat at the affiliate charter company with BWSS and used one of the BWSS captains for a day sail. Before we bought our boat I wanted to find out how my wife reacted to the motion ( motion sickness) and I was not familiar with the area. The boat left some things to be desired, but the captain was great.
As far as the boats are concerned, they are charter boats and they do get beat up if used as frequently as their owners want them to be. However, liability says that they are usually safe and clean. You are not buying the boat, just vacationing and learning on it for a week. Ever rented a condo that was just OK? Same thing. Also, when there are four student and an instructor berths are the issue. You need at least three cabins and someone in the salon to accomodate in most cases. Therefore the bigger boats, which there are fewer of, which means that they are used more.