I have had the occasional flawed sixer from some of the bigger craft brewers, but that isnt too often. Mistakes happen, even for the big guys.
That being said, Breweries are popping up all over the place. The craft breweries ive been to here in Denver are putting out some legit beer. I've noticed the beer from brew pubs - restaurants and breweries in one, in general arent as good as the smaller craft beer places that focus on beer alone. My guess is that they have to focus on the food more so than the beer to be successful. I think most of them will hire a guy who has been through a course to run the brewery. None of the courses I have looked at (and ive looked into several) go over how to truly formulate a recipe. They do cover science, systems and all though. This may be part of it. A guy running a brew pub might not have the best recipe sense, and is throwing in some off combinations resulting in off beer, compared to others. If the brewpub is corporate, the guy brewing the beer is just running the system. No creativity on their part, just corporate recipes, whether they are good or not.
I have also seen some brewpub systems being sold where they provide all the equipment, and some crash course training, then send you kits to make different beers for your restaurant. I doubt these kits produce award caliber beer, and operator error is more likely if the guy isnt a serious brewer. I think a lot of places outside of the big beer areas are going to run into this type of setup, at least for a while.
The beer boom is going, I'd sure like to get in on it, but its going to be like restaurants, where there are great ones, OK ones, and lousy ones. The consumers will sort it all out eventually.