What exactly is a flagship store? The main store in a population center of perhaps 500k or more people?
Flagship stores are generally the larger ones with special amenities. Doesn't have to do with population size, but usually they're in populated areas.
I can't find a list online, but it is a designation Apple uses. Examples are the Fifth Avenue Store in NYC, Union Square in San Francisco, U Village in Seattle, and Pioneer Place in Portland.
They've typically been the first to adopt the town square design, have kept the theater area for demos, etc.
They're typically not found in indoor malls.
Here's a USA Today article that talks about what usually designates a flagship:
Apple is 1/3 of the way through major remake of flagship retail stores
Flagship stores refocused as education first, sales second, in bid to win customers for life.
www.usatoday.com