I think the current contracts are about two things: perception of worth and Amazon's market share.
The BPHs are desperately trying to avoid the iTunes scenario. Jobs successfully took control of pricing away from the music industry. Thanks to him, a song is worth $0.99. Forever. It's branded into the public consciousness. Although if you're willing to forego owning the song, you can go even cheaper.
The BPHs *really* want to avoid giving Bezos control of what a book is worth. They've only been partially successful. That's the danger in dealing with a retailer that cares more about market share then profit. I'm pretty sure the BPHs fear an Amazon monopsony, and I don't think they're wrong to.
And speaking of Amazon market share, combating that is another reason. Agency has its faults, but it does allow for a range of retailers, even if those retailers can't cut profit margins to the bone like Amazon does. (Kobo, for example, is reliant on Agency to the point that they've lobbied to keep it.)
I honestly don't mind Agency, as long as the publishers aren't idiots. (Sadly, not always the case.) If I can get my e-book for a little less than the mass-market paperbound, I'm okay.
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