First of all your puppy is really cute! There is just a standard size for all yorkies reguardless of registration. At one time I didn't know what the differences were in all of the registries. Even though many people do not like AKC, they do seem to have higher stanards for their dogs than the other registries. I have heard that lots of pets shops and BYB's tend to use registries other than AKC.
This is a thread about AKC vs ACA. But don't be fooled just because a pet shops calims AKC, some bad pet shops still use AKC or give bad paperwork.
http://www.faqs.org/qa/qa-1134.html
A good website that compares pet shop pups to good breeders.
http://www.kerryblues.info/index.htm...PETSTORES.HTML
Don't be upset about your pup's size or registration now though. As long as you love her then none of that stuff matters!