Amazon and online retail are actually a huge sociological problem in this context. If you can just order manga you like, and form bonds w/ online communities of folks w/ similar tastes on tumblr or twitter or wherever, what's the incentive to go to a physical place in your town?
Gaming stores have reinvented themselves as places to play games with others, but it'd be an interesting challenge to reinvent comic shops in that same way.
In the New England area, I think Newbury Comics has done a good job of reinventing itself -- it wasn't ever (in my memory at least) just a comics store and made a lot of its money from music for a while, but if you go in there now it's got some movies, music, a comic section/room, but it's mostly other stuff -- merchandise from trendy games, shows, movies etc. Funny/quirky gifts, toys, jewelry, etc.
Maybe doesn't appeal to die hard comic book fans, but it's a fun experience for the casual shopper, which makes it viable. My 12 year old is always excited to stop in there.
Gaming stores have reinvented themselves as places to play games with others, but it'd be an interesting challenge to reinvent comic shops in that same way.