If I want to buy a book, i'll go to Amazon and buy it. With kindle, i'll have it in 10 seconds. If its not available on Kindle with Prime i'll have it next day. You can't compete with Amazon. So its not worth trying.
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.
If it helps, I upvoted your other comment :-) If I had a cafe, I'd love to try the referral thing. There has to be some solution for the future that makes it possible to go to a shop, pick a nice book and sit down with a coffee.
Their goal should be a strong marketing push in a niche market, specifically focusing on the community, as there's plenty of room for players in the space. There are a lot of people who hate Amazon (not really sure why; hatred of the big guys, I suppose?) enough to allow for these competitors to thrive. I think Powell Books in Portland is a great example of such.