I went through the same dilemma. Stella was in the pet store when I went to buy my parents' dog an Easter outfit at Easter, and when I went back a month and a half later she was still there, and I felt so bad for her. Now knowing how bored she gets when she's alone for 15 minutes--I can't imagine her being there for that long!
Since we had been looking for a Yorkie from a reputable breeder for over three months with no luck (they all blame the economy for not having puppies, which I understand, but...we got a lot of negative attitudes too, which I didn't like), we decided to save her from the pet store since the local store at least had a good reputation and Stella's personality was stunning--not to mention ALL of her routine visits and vaccs at a great vet clinic for the next 10 years are free. I'm happy to say she's in great health, and the vet was very impressed with the health of all the potential problem areas--teeth, knees, spine, etc. Sometimes it just works out best for you and the pup