Lucky Ocean - Pro: Usually health stock, if things do get sick/diseased he will actively treat them before selling, prices comparable to 6th avenue on many items. Cons: Not a terribly large selection of corals, if you're into SPS then probably should look elsewhere, although getting minicolonies is not out of the question.
Tropical Reefs: Never been
Ocean Treasures - Pro: Friendly, large stock of items, store looks uber cool, lots of corals to choose from. Con: Parking is a pain, do NOT park in the lot next to the store the owners of that lot have been known to lock the gate with cars still in there.
Aquatic Central (Ocean Avenue) - Pro: lots of nice little things, fairly cheap on invertebrates, some corals are a good deal. Con - Fairly small selection of fish (although they have a downstairs area that is supposed to open up more room), some corals are priced for their rarity (ie no finding a gem in the rough and getting it for a steal of a price), occasions I've been in the staff has been more concerned about tank related items (although if you ask for help you can get it, but I'm the type of person who likes the merchant to give me a "If you have an questions just ask" type feel).
East Bay stores... yeah I would say at one time all the better ones were over there, but stores are closing up all over the place so don't think this applies as much. The bonus of the east bay stores is they have room to expand (cheaper rent per sq.ft)