From what I’ve heard, there are very few (if any) puppy mills that do treat their animals well. They breed their bitches too often, which causes health problems. They aren’t always as careful with which animals should be bred as a good breeder is, which can result in genetic problems with health or temperament for the puppies. Puppy mills don’t always do as much socializing of their animals as should be done to get a pet with a good, friendly temperament, either- socializing at a young age is very important for the temperament of puppies or kittens. A puppy or kitten that isn’t socialized to humans young isn’t likely to grow up to be a friendly animal that isn’t afraid of people (and if I’m getting a puppy or kitten, that’s the kind I want). And puppy mills sell their animals through large distributors, and the people at the pet store who sell the animals generally don’t know anything about conditions at the breeder that bred those animals, so you as a buyer can’t know either.
Even if a puppy mill did treat its animals well, and I had some way of knowing that, I would still have a problem with pet stores that sell animals. Reputable breeders generally want to know quite a bit about who’s getting their puppies before they will sell you one. They want to know if you will spay or neuter the dog, what kind of training you will get for the dog, where on your property the dog will live, stuff like that. And they will make you sign a contract, so they could take back the dog if you say you will do something (like spay or neuter it) and then don’t do it. If you buy a puppy from a pet store that sells them, the only question you will generally be asked is “can you pay for this animal”. I think letting anyone who can pay for it have any kind of dog they want is a bad idea (especially for breeds that can be dangerous, like pit bulls or any large breed dog). I would be against a “no-questions-asked” business model of selling puppies even if the puppies and their parents were very well treated by the breeder, because of the problems that happen when people who shouldn’t have certain kinds of dogs get them. Problems like neighborhood kids getting mauled to death by poorly-trained large dogs… And then there are lesser problems for the dogs, like an energetic dog (such as a border collie) being sold to someone who lives in a tiny apartment and doesn’t want to spend much time exercising the dog.
If you’re willing to buy a dog or cat when you know nothing about health or temperament problems it might have, go to the animal shelter and get one there- that way, you’re saving an animal that might otherwise be killed. It will probably also be cheaper than buying an animal, especially a large dog, from a pet store. A shelter adoption fee is also more likely than a pet store price to include necessary medical care like worming, shots, and spaying or neutering.
If pet stores did make sure they bought puppies and kittens only from a breeder that treated its animals well and paid careful attention to genetics when breeding, and did properly socialize the animals, and did do some screening on the people who get their animals, and did keep the puppies and kittens in their stores in decent enclosures, I wouldn’t have a problem buying from them. But I don’t know of any that do those things (if one did, they would presumably advertise it, to get business from people who are concerned about puppy mills). So I won’t buy anything from stores that sell puppies or kittens.
Stores that have dog and cat adoptions at the store are a whole nother story, of course. I’m quite willing to buy pet supplies from a store like Petco or Petsmart that provides space and time for people from a local animal shelter or rescue group to show available animals and do adoptions.