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.