Actually, it does make a huge difference if a puppy is registered with AKC or APRI.
When the AKC toughened their requirements to register and started to require DNA testing, many "alternative" registries were formed. These registries are used by puppy mills and backyard breeders, those that can't meet the stricter requirements of the AKC.
Getting a puppy with papers from one of the alternative registries often does not even guarantee that the puppy you are buying is purebred. APRI, for instance, registers 'those that do not have documented pedigrees.'
It's buyers beware if a breeder registers her puppies with another registry besides the AKC. Please read this article to find out which registries to avoid in your puppy search.
http://www.nppmwatch.com/AKC.html