I also didn't know Borders had a bigger stake in the market. Walking in to one or the other, you can tell one store is for yuppies (B&N of course), and one is for everyone else. The prices are the same, because no one buys the idiotic 10% off member cards, and both rarely offer a sale price on anything, opting for the ridiculous prices printed on the backs of the books.
Borders has the better atmosphere, with clearer, easier to read shelving (i.e. Fiction, Magazines, Movies). The worst part of any bookstore is when you find out it's harder to navigate than a library.
If I had to choose between the two of them, in terms of what I'd want them to look like if they merged (which I see no proof of in the story, and not even an official comment), and how I'd want the employee attitudes to be, I'd go ahead and choose Waldenbooks.
I always go with the underdog, because they're more motivated to not shove subscription cards down your throat every chance you get.
