EmptyYourMindBeFormless, I could not have said better.
It's sort of a gamble with pet store fish. They may be wonderful fish, very healthy and beautiful. But you just don't know what you're getting in that gene pool if you were to breed.
So if you're weighing say an aquabid fish vs a LFS or chain pet store in your area it really is going to depend on your goal. Meaning, if you're only looking for a pet fish, no breeding or anything fancy then a pet store fish would be fine. If you want to breed then going through a breeder and paying good money is a better option. You generally get what you pay for.
There are exceptions though, as always. You aren't 100% promised a healthy fish from a breeder and you're not looking at a high rate of poor fish from a pet store every time either. Pet store fish can sometimes be breeding worthy as well. Some members here have found spectacular bettas at Petco.
That being said... I saw a betta on aquabid tonight that was bid at $500 and $1000 buy-it-now. That is waaaaay much for a fishie!! He was pretty though.