This is the very worst option of all, bar none. At least with a backyard breeder you can usually see the puppy's parents and see if they at least vaguely resemble the breed they're supposed to be. Pet shop puppies come from puppy mills. Puppy mills are regularly closed down when health or animal welfare authorities investigate and sometimes the horror stories even get in the media, though they generally stick to dog bite stories. Puppy mills and their clients exist to make money.
Problem is, they are treating dogs as a commodity.
Fine with soybeans, gold or oil, personally I object to it in pets. Refuse to do business with any store that sells puppies on site and tell them why. If stores find doing business with the mills more aggravation than profit, they'll stop, otherwise they won't. Boycotts are being organized. There is nothing more important you can do to help dog overpopulation than to spay or neuter your pet.