I found an interesting blog post by Michael Stackpole on the switch to the agency model. It's worth a read.
An excellent post by April Hamilton over at Publetariat.com got me looking at the actual numbers on the money paid to authors under the old system for the Kindle, and the new Agency Model. Under the old model, ebook royalties were still connected to the cover price of a physical book. Under the agency model, they are linked to the retail price of the ebook. In both cases the author gets a cut of what the publisher receives.
So, the great victory over Amazon actually costs authors money.