The advantages of buying directly from a reputable breeder cannot be overstated.

If you buy a snake from one of these chain stores and two or three months later, you have a problem, they probably aren't going to be of much help. Most pet store employees being high school age kids, who are generally not well educated on the subject of reptile husbandry. I assume that they have a high turnover rate and you may not even be able to speak to the person who sold you the snake.

If you buy from a reputable breeder on the other hand, you'll be able to go back to that person at almost any point in time if you have any questions or concerns regarding the proper care of your animal. And you'll be able to rest easily knowing that they most likely have a pretty decent understanding of the animals in question because they are in fact the ones producing the animals.

Essentially you'll pay inflated prices for sub-par services when shopping at a chain store. I'm not saying it can't be a good experience, but I would cut out the middle man.