I think having a friendly staff is at the top of my list. Then, no smells. Went to an LQS on a shop hop. they had a cat, and the place stunk. Got my block, my stamp and left (threw out the block at the next location -- it smelled too).
Don't like the 3-high bolts (I'm too short to appreciate them and the bolts tend to fall on my head when I try to take them out.) Like fabric organized by type -- put the flannels together, and the batiks, etc. I don't mind a mess if it organized, but the fabric must be clean (and sitting on the floor is not clean to me).