There are many reasons not to buy a pup from a pet store. The parents are not available to scrutinize, so you don't know what the pups will look like, or if they have health problems, etc. In fact, many times, it's more than you'd pay for a pet-quality pup from a reputable breeder. Honorable breeders begin training pups, socializing them, and spending quality time with them. No pet shop can afford to do this, and a cage isn't the place to raise a pup, anyway.
Conditions vary from many different breeds in pens to thousands of dogs in rabbit cages.
The most popular breeds are bred for a profit. Reputable breeder - a knowledgeable breeder who's purpose is to produce the perfect specimen of the particular breed. All others are spayed or neutered so that the bad traits aren't passed down to future generations.