When I first started visiting San Diego in 1992, downtown was full of bookstores. There was a whole gathering of them up near and off Broadway, including Wahrenbrock's Book House, the used bookstore that held out the longest. The side streets near its Broadway location where dotted with smaller stores and there was even--for a couple of years, at least--a comic book store in the same general vicinity. All of them are gone now.
Horton Plaza had two major bookstores (three, if you count Le Travel Store, which had a large travel book selection, and was also in HP back then; it currently exists on Fourth Ave, and still has a nice section of books), a Doubleday (which is also sadly gone from New York City...one of my favorite Fifth Ave. bookstores there) and a B. Dalton. After a while, I believe the Doubleday turned into a Waldens, which went away when Borders (the corporate parent of Waldens) opened downtown in 2004 or so, in a building they built at the corner of G Street and Sixth Avenue. That building--which I drive past every day on my way to the freeway that takes me to work--is now sadly--forlornly--empty. A narrow Borders sign hangs from its G Street side, marking a kind of bookstore ghost town, or ghost building at least. It's a shame, both from the standpoint of no bookstores downtown, but also because it's a beautiful building.
B. Dalton closed in Horton Plaza a year or two ago, to be replaced by a Crown Books. Someone evidently bought the Crown name, which was a chain of bookstores here in California (and possibly elsewhere, for all I know) when I first moved out here back in 1998. There were at least three I frequented, because they had huge discounts at that point in time. The new incarnation of Crown can also be categorized as a discount bookstore, but it unfortunately only features remaindered editions (if you need a copy of Frommer's Unofficial Guide to Disney World, 2005, they have you covered) and books that probably should not have been published in the first place. (Seriously...one of the 2011 calendars they had on display pre-Christmas was titled "Rats." I'm assuming it wasn't a best seller, but I was shocked enough to grab a photo of it, since I figured no one would believe me. Maybe it's big with research scientists. Or cats.)
There is one small bookstore in the touristy enclave of Seaport Village, down behind the waterfront hotels and the Convention Center. It's called Upstart Crow, and while it has a small but nice selection of books, it also has a large amount of tourist claptrap. The nearest big bookstores to downtown is the still-existing (but don't blink) Borders in Mission Valley, the Booksmart in Point Loma, and a few remaining used bookstores in Hillcrest, along Fifth Avenue, between University and Pennsylvania. There's also a Barnes & Noble in Hazard Center in Mission Valley.
And that's all folks. The world of books in downtown San Diego has dwindled away to nothing. Some may call it poetic justice (pun intended) that the chains have fallen apart. I call it just plain sad.