As as side project I helped a friend publish a small book on Amazon for the Kindle. At the time we looked into doing the iBooks Store, but it was not yet open to self publishing. Apple's requirements for pricing were as follows: 1. You could set whatever price you wanted. (e.g.: Apple doesn't fix the price at anything specific) 2. If you sell the book electronically elsewhere, you cannot sell it on iBooks Store for m…
Under the agency model, the publisher sets the retail price instead of the wholesale price. So Amazon now has to sell it at that price. This is probably different than the deal you got with Amazon since you don't have the leverage that the big six have.
The agency model also includes other stipulations to protect the traditional publishing model. One example is that many eBooks don't launch for several weeks after the hard cover books. My understanding from listening to Robb Wolf and Tim Ferris talk about their recent book launches is this helps the NY Times Best Seller rating in some way.
As a consumer, I use Amazon for their discounted prices. Recently when I wanted a book, I could pay $49.99 at the local B&N or $32.95 at Amazon plus $3.99 for one-day shipping. However, had I wanted to get the same book in digital format, my options were $39.99 at Amazon or $39.99 at Barnes & Noble.