I think the only real benefit to independent bookstores anymore would be those with specialized collections: a feminist bookstore, for example, or one that (as mentioned above) specializes in comics and media tie-ins. General purpose independent bookstores can't compete with the big box stores, who can't compete with Amazon.
In general, I know what I'm looking for when I go to Amazon. There's a very nice local indy store that I like to go to when I'm looking for non-specific non-fiction like science or psychology, and I know they have a small but choice collection there.
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