There is not common average in quality and care between a single chain of aquarium hobby stores unfortunately.
I'm glad to hear that you're concerned with the care and health of the Betta's in the store!
Most people think that keeping this fish in small bowls and vases is alright and good for them, but it never occurs to them that it really isn't. These fish don't live in mud puddles as so many people say, they live in rice paddies, and really it's not even these fish, because the ones you see at the store are have been selectively bred to be the way they are, their wild counterparts live in stagnant rice paddies, not in muddy water puddles.
Container size does not always mean that these fish are healthier or more apt to be a better fish for you, though it's great to see a betta in more water because he or she is going to be so much more active and energetic, assuming that it is a healthy and well cared for fish. Walmart might have larger containers but if they are not changing the water and allowing waste to build up, then your fish might have more room to swim but he is still going to be less healthy than a fish who lives in a smaller container and gets frequent water changes. The small containers they live in, it is suggested that they should be changed four or five times a day because the water is fouled so quickly. If your concerned about the health of these bettas, ask the aquarium representative about the water care and feedings of these fish. For example if they are over fed, they may be constipated, which isn't a difficult thing to get over, but it does cause a lethargic or seemingly unhappy fish.
The Petco that I go to to look at bettas on occasion (I generally get mine from breeders but you can often find a nice little male or female at the store if you look hard enough), have them in small containers, but the water is changed out two or three times a day. The walmart near my home has bettas in small containers, with blue or violet water, and these containers are obviously very dirty and polluted from over feeding and waste build up due to no water changes. As for the smaller females you come across at petco or petsmart, keep in mind that its very possible these little girls could be very young fish, they're not born already 1.5" or 2" long. The age of the stock is obviously going to determine the size (not that I'm saying that proper care doesn't have a say in the size of a fish). This goes for the males too, larger males are going to generally be older (it also depends on the variation of the breed, but sticking to a more generalized rule, older fish tend to be bigger).
Like people have been saying before this, it really depends on where you're going, because sadly the fish care varies greatly between even one select chain, like Petco for example. Don't let it turn you off to these fish dealers totally, just keep an open mind out and venture out to other Petco or Petsmart stores, or flip through the phone book and look into local aquarium hobby stores, near where my boyfriend lives, we've found a great chain and they bring all their betta stock in from local breeders, it's a little more pricey but you get a nicer selection and the bettas are all kept in nice glass bowls, larger than those little pint size plastic containers, the females are kept in a large 29G tank, separated by variation so you can find all your halfmoon females in one place for example. Even their fish rooms are very clean and well cared for, there is not a sick fish (or dead fish for that matter) to be seen, and they do house quarantine tanks in the back from what I understand.
Just search out an aquarium hobby store that meets your health fish health standards if your that concerned. If the Petco 5 miles away has poor fish care, take the time to check the Petco 20 miles away and so on.