What I look for in my lfs:
-Friendly and helpful but not pushy staff.
If I'm asked what size tank I have, I fully expect to not be offered a lionfish for my 20 gallon.
-Stock that moves through the store fairly quickly. To me, this means the store knows it's
market and no fish or coral is left to languish in sub-par conditions or care.
-Adequate lighting over the coral holding tanks.
-Reasonably clean. I don't mind dust, but leaks that are always there worry me. Piles of dusty maintenance equipment pushed off in corners are also worrying.
-Algae free frag tanks! Bits here and there that I can remove by nuking the plug in peroxide are ok, but furry plugs are a no-go.
Even though I have these requirements, I usually take what I can get. LFS near me are very few and 1.5-2 hours away. Luckily the ones in my range are quite nice! There's a very nice one 4 hours away... I visit the 1.5 hour away one once a month, usually at the same time as my Reef Club meeting.
My local petco has a very involved aquatics manager that's been working hard to improve her store. She'll happily arrange for livestock to be in for you to pick up from the bag, and special order particular things for you. She told me recently that she's been given the ok for a larger number of things to order from, so I can expect to see better variety soon! She jokingly suggests tangs and angelfish for me everytime I see her though, and shows me a bumblebee shrimp almost every visit.