I have to add my vote to the chorus of Bay Area gamers singing the praises of Gator Games. Great slection, and staff that's at least moderately friendly. Neutral Ground had been degenerating for a while, IMO; I think they shot their wad when M:TG was super-hot, and rented all that floor space for tournaments, and so have a more limited cash flow now, even with getting rid of half their store. I'm sorry to hear about Scenario in Fremont (a few blocks down from where I used to live); I liked how it had a very nice selection of RPGs and CCGs, even though they were obviously more of a model trains and model cars type of place.
As for Chicago, I've been impressed with Games Plus. I hadn't heard of them until the ENworld get-together was announced, but I've been there several times since. I happened to visit both Games Plus and the NYC Compleat Strategist in the same week around Christmas, and was surprised that a store in Mt. Prospect, IL had an equivalent selection - with more square footage! Definitely better than Pastimes (Niles & Glenview), which I had been frequenting before.
(edited for my p***-poor typing skills this early in the morning)