The first big chunk of value added for independent bookshops is that they are not Amazon. That is enough for me. I avoid Amazon. But there are a few possible other pieces of value to add that the other sellers might add, but they are not doing it.
How about, if a bookseller does absolutely no business with Amazon or any of its affiliates, ever, they advertise that so that I can favor them with mine. That would be a value-added.
Now, I have bought many used books from Alibris, since I stopped buying from Abebooks when I learned that Amazon owns Abebooks, but now I find that Alibris has a deal with Amazon to ship the books that I buy from independent booksellers who list on Alibris through Amazon's shipping system. And part of the deal seems to be that any bookseller who lists both on Amazon (or abebooks) and on Alibris always lists the book a little higher on Alibris, and shipping always costs a little more if I buy through Alibris, too. So the independents, who present themselves as wanting to compete with Amazon, are being lured into supporting both the giant and the giant's ability to manage prices throughout the market. If an independent bookseller wants to offer any value beyond what Amazon offers, they should stay out of Amazon's network and sell used books that Amazon's network does not offer.
When I want to buy a used book that I find on-line that was published with one or more CD's included, I have often contacted the bookseller and asked if their copy of the book has the CD included. If the bookseller is one that lists through abebooks, Amazon, or Alibris, either my inquiry is ignored or the response is that they cannot access their inventory to answer my question, and that their terms of sale are that the CD might not be included, no matter how essential it may be to the value of the book. This uniformity of poor service across supposedly-competing sellers is suspicious at best, and an independent bookseller could certainly offer value added by not doing what everyone else is doing.
Bottom line is that it is possible for bookshop to be better than Amazon for some buyers, but I'll wait to see it before I believe it.