Borders wasn't a big box store until.. hmm I'd say starting 2004/2005. They were a large chain, and big corporation, yes.. but they did everything they could to maintain that "small store" vibe. Their return policy was basically "eh fuck it, return it, we'll take it.", their dress code was extremely liberal.. jesus I used to work there in ICP clothes (lordy), their coffee shop was in-house, low priced, and awesome.
Until mid 2k. Then they really started to go corporate with everything from return policy changes, "clean" dress codes, big crappy chain coffee shop. I started going to B&N after that.
As for mom/pop book stores, they never have what you want, B&N/Borders either did, or could easily order it.
OTOH, e-books are killing bookstores more effectively. As much as I love holding a real book, holding 2,500 books in my hand is even better. <3 my Kindle.