I'm not saying all pet stores mis-handle or don't care about their puppies. However, I have a high standard of ethical breeding, and selling to pet stores does not meet that criteria, mostly because the breeder is no longer able to control or have input in the future of that puppy, with a spay or neuter contract for those puppies that are not of breeding quality. Being "registered" does not mean the dog has the temperament, health, history, coat type, and body structure to be bred.
With ethical breeders, they are invested in the life of their puppies, for that puppies' lifetime. If an owner has to get rid of their dog at any time, the breeders welcome and INSIST, through contract, that the dog goes back to them to prevent them from ending up in bad situations. They are there for guidance to the owners for training issues, behaviour problems, etc...for the life of the puppy. Find me a pet store or back yard breeder that does that. Rare, to say the least.
Seeing a vet is VERY different than having health tests done on the parents before they are ever bred. A breeder that does not do such health tests is not a good breeder in my eyes. A breeder that doesn't have a waiting list of potential owners before they ever breed, is not an ethical breeder in my eyes. Just my opinion.
There are far too many badly bred dogs out there and far too many in need of home in shelters for me to justify or support "back yard breeding". Either do it right, or don't do it at all. That's my stand.
I'm a groomer, I see dozens and dozens of dogs a week. Tossing out some wide numbers here for the sake of example, 90% of them come from pet stores or back yard breeders. 80% of those have temperament problems, health problems, skin and coat problems. In contrast, the few that actually get their dogs from ethical breeders have well-adjusted, healthy, dogs with gorgeous coats. Part of this is how well the owner cares for their dogs (quality food...none of that science diet and iams crap) and proper training and socialization, but a large part of it has to do with the fact that the dogs' parents and grandparents and great-great-grandparents had good genes that were carefully bred.
Someone will inevitably reply to this arguing that mutts are healthier than purebreds, and I won't dispute that. However, a puggle or a shi-poo or all those other designer breeds...are not mutts. They are badly bred, INTENTIONAL mixed breedings. It takes many many years for a breed to become a stable breed. Yes, all purebreds are a mix of some other sort of dog to create that breed, but it also didn't happen in a span of 10 years, which is why Labradoodles and Puggles and whatnot are no-where near becoming a stable breed.
Which brings me to actual mutts. A true mutt does not have generations of "careful" breeding behind it to create it. A vast majority of purebred dogs DO have health problems....because they come from unethical breeding situations where the stability of that breed has long since been altered by bad breeding. Finding a truly ethical breeder in the united states today is very difficult and that is very unfortunate. It only takes ONE generation of bad breeding to forever alter that line. One puppy with bad traits being bred, and you have ruined generations of careful selection. Thus why spay and neuter contracts when selling pet-quality versus show-quality puppies is so important.
If you want a purebred dog....adopt. There are tons of breed-specific rescues out there and those dogs need loving homes too. Same for mutts...walk into any pound and you will find dozens of wonderful dogs. Why ANYONE would rather support pet stores and back yard breeders versus rescuing a dog in need or finding an ethical breeder is beyound me. I chalk it up to ignorance (and that is not meant to be an insult).
Just like some pet stores will sell a ghost knifefish to a person with a 10 gallon tank and not think twice, whereas another will educate and even refuse to sell if the tank is not sufficient. 
