I'm not fan of BD, being in the LBS business, but I do have to say that we get bikes from major manufacturers that have the same problems. The difference, of course, is that we disassemble the bikes and build them back up before you buy them.
Lots of people are shocked that shops charge $120-$180 to build up a bike that was purchased elsewhere. This is why. To completely disassemble a bike, chase all of the threads, hone the seat tube, grease/lube/locktite everything and true the wheels, takes at least 2-3 hours. Our shop rate is $60/hour. Ergo, the $120-$180 assembly charge. Add that to your BD purchase price.
Most shops give you at LEAST one free tune up. We give one free tune up and the occasional free adjustment with our bikes. We also provide a comprehensive, computer-imaged (NOT computer-suggested) bike fit free with the purchase of a bike (or $285 without bike purchase). This is a 2-3 hour bike fit that includes an interview process, a video recording of your form and style on the bike, all adjustments and replacements as needed, and aligning and shimming (if required) of your cleats for proper foot angle.
Add that to the cost of the BD bike as well. Does it still look like a good deal?
How about the fact that you never have to call, email, or post on a message board for days/weeks to get a warranty issue resolved? You can just bring your bike in. If it's a part malfunction (such as a BB) chances are we'll just replace it from our own stock and deal with the warranty crap later. Result: you get back on your bike quicker.
Too bad we (LBS) "rip you off" so bad.....