Why Buy from a reputable breeder vs pet store
You know the health of the puppy from birth.
References: a responsible breeder will have references whom you can check and see if this is the right breeder for you. Most of the time the pet stores, in general, have limited knowledge about the breeder, or don't even know the breeder of the dog they are selling.
Responsible breeders find a home for every dog they breed.
You can see the pup's parents via photo, video or in person in some situations. Many times pet stores do not offer this service since they are all about making the sale.
Reputable breeders screen perspective pet parents instead of taking anyone with cash or a credit card. The reputable breeder will take the necessary steps to get the pup into the proper situation. Most pet stores it's about the sale not checking references.
Many breeders like to stay in touch with the pet parents who adopt one of their pups. This is a good resource for the pet parent being able to reach out and ask a question from time to time about the pup, or breed. The breeder is a resource of information and may have experienced a similar situation at another time.
Breeders many times can recommend veterinarians who understand and know their breed. Some breeds have specific health issues you should be aware of before bringing the pup home.