It isn't the agency model that is the problem, it is how the Apple et al. coerced/enabled the publishers to price-fix and then allowed/enabled the publishers to impose that price fixing on Amazon. I still don't exactly understand why Apple and Google are being sued and not the publishers.
[edit] It is Apple and five publishers according to the WSJ: "Three of the publishers have agreed to settle, according to court documents. Those are Hachette Book Group, Simon & Schuster and HarperCollins Publishers Inc. Under the settlement, those publishers will terminate any agreement they have with Apple regarding electronic books." http://online.wsj.com/article/SB1000142405270230444460457733... [/edit]
Money quote:
Along comes Apple and the iPad. Steve Jobs talked the publishers into the agency model - publishers set their own prices and they get 70% of the proceeds.
[...]
Publishers then turned around and imposed that agency deal on Amazon, which is the subject of the DOJ investigation [the agency model, not Amazon - gvb]. The end result: There really is more competition in the e-book world, but prices are higher than they likely would be if Amazon and others were able to discount as they saw fit.