Terrierman's blog and website are worth a look for a perspective on working dogs and the few breed organizations which actively try to limit and/or discourage the type of inbreeding that is all too common, and perhaps nearly universal in kennel club "show" breeds.
The involvement of the AKC and prominent breeders with the AVMA and some veterinary schools is another area where scientific evidence is falling short in the world of veterinary medicine. Organized veterinary medicine has been strangely silent on the problems associated with the inbreeding of pedigreed dogs. Terrierman seems to have a valid point that financial interests (support of veterinary schools, the AVMA, providing pet insurance, etc) by kennel clubs is suppressing criticism of bad breeding practices by the veterinary profession as a whole.
I think that changing current breeding practices has the potential to improve pet health more than nearly anything other than the development of effective vaccinations did. Many common problems in purebred dogs and cats have dramatically different incidences in different breeds, suggesting strong genetic influences on these diseases. Scientific veterinary medicine can and should encourage kennel clubs to change current breeding practices which result in so many unhealthy dogs being sold to the public. It is also interesting that the AKC pet insurance automatically excludes "any congential/inherited condition" from coverage, while encouraging breeding practices which lead to exactly these problems.
Another interesting aspect of this subject which seems to tie into this topic is the promotion of unproven therapies (Complementary, Alternative and Integrative medicine) by many breeders and in some of the AKC publications. I wonder if the seeming affinity of kennel clubs for CAM is a little extra smoke and mirrors to distract people from the real causes of so many of the problems in purebred pets. These therapies are indeed often promoted in publications such as Veterinary Economics as a good way for veterinarians to increase their income. While I don't agree with Terrierman 100% on his recommendations on vaccination (he goes a bit farther than current evidence would indicate, but not by a whole lot) and a few of his other medical advice, I understand where he is coming from and that his recommendations are a response to many veterinarians who make decisions on vaccine frequency, parasite control, etc. based on what is best for their income, not necessarily what the evidence supports.
I think kennel-club endorsed breeding practices are indeed an area in which the science and evidence based veterinary community could make a difference in the lives of animals and the practice of veterinary medicine.