"Last I checked, an "independent" bookstore was run independently and not as part of a chain."--That's a convenient definition that many people use but that I think is bunk. If you, a bookstore, are getting and carrying books from mostly traditional distribution systems, from mostly big publishers, from mostly the same-damn widely lauded and published writers, you're not really an independent bookstore. On that essay I linked to, as I implied, independent bookstores should also be venues for INDEPENDENT WRITERS primarily, not for commercial writers primarily, not for well-known-and-now-connected literary writers primarily.
First, you don't get to make up your own special definitions and then castigate other people for not following them. An independent bookstore is a non-chain bookstore.
Second, independent bookstores don't follow your very special definition because it's a recipe for a quick financial death. Most people want the stuff on the bestseller lists. Even at specialty stores, mainstream books are the backbone of the operation. Booksellers bemoan this and do everything they can to draw attention to offbeat books--even the Borders store near me has a staff picks section, and it's full of wonderful and quirky stuff--but the truth is that bookstores must stock mainstream books because mainstream books are what sell.
If you want to see more self-published books selling, there are a couple of things you can try:
1. Open your own bookstore. You can even do it online for the cost of a domain name. Create an independent bookstore to your own recipe, and see how you do.
2. Review and promote more self-published books. You say over and over that the self-published work you read is almost as good as the traditionally published work, and sometimes better--so tell us what these gems are! People wouldn't be so averse to self-published books if they could find some good titles. If you're not willing to share what you know, the rest of us are going to keep thinking that self-published books (including yours) all look like this.