Actually there are some gorgeous fancy guppies at my walmart. I think they're the same as stock that petstores sell, so they're the same quality. Of course the difference comes in how each pet store deals with their fish, their care and how well their employees know about the fish. Walmart is a great place to get "stuff" but I'd be careful getting fish out of their tanks...do a good check for fish that have any sign of disease or wierd behavior in ANY of their tanks, and quarentine new fish when you bring them home like usual.
I'd say a local petstore who takes good care of their fish or specializes in a certain kind of fish would have the best quality, and also charge the most.
Petsmart would probably follow them...most of the petsmarts I know take pretty good care of their fish, even if their employees don't know as much.
Then Walmart...as you pointed out their employees don't know much of anything about the fish and I think they are paid less attention as far as care goes.