Good question! I have 6 favorite LQSs. Mostly I go back because I'm friends with the owners. They're all friendly, have great fabric selections, etc. They also tend to be local quilter hang-outs with coffee and places to sit and chat.
The ones that aren't my favorites are just stores, not shops. You may or may not get greeted when you go in.
The one I refuse to shop at is mostly an internet store but she's supposedly open evenings and saturdays. She belongs to a couple of guilds I'm in and thinks she's an authority on nearly everything. Plus she's selling a kit to guild members for a guild workshop at full price and acting like she's giving them a discount. I've seen the exact same kit advertized for less in a couple of magazines.