I've always been able to get some good merchandise deals (tanks especially) at the one here in Columbus, just buy the stands elsewhere or make your own...I hear a lot of people complain about merchandise prices, then I go to other stores and they're all about the same if not more expensive, so those people are either mostly delusional or shop online all the time. Also, it never hurts to ask about getting a better price, if you're buying several items, they seem pretty willing to help you out some on the price...I've gotten deals when buying multiple items for the fishroom...more is less, so to speak.
I hadn't heard that about the AA in Chicago being a joint Petland and AA (if it is I hope there's some way to keep the two halves separated). By the way, Petland owns the name, but nothing else, I heard they sold the AAs they did own a while ago but are trying to open a couple corporate owned ones again for some reason (not poorly managed enough, perhaps???).
I have heard some good things about the AA in New York. Different owners, different management, different results. It might take a while to shed the corporate BS and evolve into their own store in Chicago, but I'd at least give it a chance...and maybe wait about a year before you visit it the first time, gives things time to settle down and age a bit. I heard from a couple friends that when the Cincy store opened, they apparently thought they were the only game in town and prices were 2 or 3 times what they would've been in Columbus (keeping in mind there was a grand opening "sale" this reduced the prices a little bit). Anyway, I guess the prices are more normal now since nothing sold the way the prices originally were (normal for AA at least).
In my opinion, AA caters more to the casual hobbyist. There's a lot of "Awe" factor in some of their displays and the general size of the store (definitely worth a stop in to look around). Newcomers will be impressed at the displays and turned on to setting up their first aquarium just by walking around at the store (a delayed impulse purchase more or less). Of course, most newbies I think are inclined to return to the store they originally purchased their aquarium from, as it's a familiar setting and chances are they already looked around and picked out what they wanted. So you capture people with the displays, and then make them happy enough to keep them coming back for a while.
I guess I'm the odd man out here though, as I don't have a total disdain and hatred for the store...I just know what's worth buying from them and what isn't. I avoid the crap and buy the stuff that's a deal. Also, I hear a lot of people talking about the shaky advice. Some employees seem to know more than others (and yes, some advice is absolutely horrid). It's not always easy to get experienced, dedicated hobbyists to work at an aquarium store, especially with what aquarium stores pay, but there are usually a few knowledgable hobbyists that end up working at stores like these. I honestly never go there looking for advice, so it's a non-factor for me...I always thought that's what forums like this were for anyway.
Think of the store as a big Petland and you'll probably be pleasantly surprised.