If you want to run a remarkable book store today, don't sell books. That's a loosing battle. This is where i'd start if I was trying to think of ways to innovate in this space. I'm sure you're familiar with Porter square books. They for instance have built a pretty remarkable community around the store with book clubs etc.
Other then that, i'd like to say good luck! I live in Boston, so i'll try to visit the next time i'm in the neighborhood.
Browsing on Amazon sucks. If you know what you want it is OK, but for discovery there is still room for improvement.