Depends on the shop, I suppose.
My LDS of choice is owned by the two guys who run it. They'd been working for one of the two "chain" shops in our area, and decided they could do it better on their own. To my concern, they have.
In most chain shops, you walk in the door and if you're lucky someone will say "can I help you?" At my shop, you walk in the door and it's "Hey Bob, where'd you go diving yesterday?" I don't have to tell 'em what mix I want in my tanks ... they already know. I don't have to worry about whether or not the person filling my tanks or servicing my regs knows what he's doing ... I know that he does. If I want an item they don't carry, they might help me find it ... or at a minimum they won't fuss if I choose to buy it someplace else. Most recently when I purchased a new drysuit from someone else, the two owners asked if I could bring it in so they could take a look at it. Service always comes with a smile, and if I come in with a special request, or am in a hurry for something, I can count on them to drop what they're doing and take care of me.
I don't choose a business strictly by the price of their products ... although with my particular shop I've never had a complaint about what they charge me for things I buy ... I also consider that an LDS is a service provider. I insist on good value for my money, and good customer service is worth a lot.
Biggest reason I choose the smaller shop ... it's like spending time at a friend's place. Walking into a shop where you know you're going to be welcomed warmly and the owners are looking out for their customers is fun ... which is why I dive, and why I do business with that particular dive shop ...
... Bob (Grateful Diver)