I have to say that my local Petco is actually a much better resource than any of the other LFS around. I got my frogfish from there, and he's doing fine, the aquatics people all know what they are talking about (other's in the store dont' know anything about fish, but they also don't go into the fish area). I have seem some sick fish, but to be honest, I haven't been in a fish store yet where I didn't see some sick fish. The petco guy (named Kyle) has several tanks (shown me photos on his cell phone) has a good knowledge of salt tanks, verifies everything with quotes from books, or reinforces what I've heard elsewhere.
I guess that all I'm trying to say is, that given the right people, it can be a great place. Just like if your favorite LFS got an idiot in giving folks advice or selling fish that could be problematic, doesn't mean the whole establishment is bad. Unfortunately Petco is a corporation, they hire those who walk in, and most folks don't have much skill in salt (or even freshwater) systems. I will buy from my local PetCo anyday, but there are some within driving distance that I wouldn't even put there fish into my quarantine.