My two cents on this since I do pretty much all my business with petco -currently-

Honestly the biggest problem I've seen with them is consistency- they have a knowledgeable fish expert that works at the one near my house, but the stooges that work under her have no clue about anything.

Last time I was there I spotted an albino frog that escaped and rescued it, pointed out that their blue gourami tank was infested with eye fungus, and noticed that their plant tank had become infested with snails(Ramshorn luckily).

Their selection isn't particularly great and they have pretty high prices on equipment.

Still, when they are running well they do it right. The expert here actually seems to really care about her fish and I usually have interesting things to discuss with her.

Overall I'd say that they get a C for fish and fish supplies. Worlds better than wal-mart, but the store is just way too generalized for them to really be a top quality aquarium shop.