Once Agency pricing goes the way of the dodo bird, Amazon will once again resume undercutting everybody on price. That's just reality, and anyone shopping purely on price is probably going to be happier in the long run with Amazon and their loss-leading $9.99 deals.
I recently examined the NY Times top 10, and compared the pricing at three big stores, including Kobo and Amazon, and the pricing was identical across the board except for two HarperCollins titles, where Amazon was cheaper than Kobo and B&N.
So going forward in the short term, pricing is going to be determined mostly by publisher policy, and somewhat by Amazon's ability to drop prices again from select publishers. In the long run, Amazon's plans for world domination will mean that anyone shopping on price alone should just go the Amazon route.
If anything good can come from Amazon being the WalMart of e-books, it will be forcing publishers to come down on their wholesale price because Amazon won't bleed money forever.
In another test, I examined the top 30 titles in a particular specialty, and looked at their pricing in Kobo vs. Google. For some of the smaller publishers, Kobo offered okay discounts. On some academic titles, the needle went back and forth between Kobo and Google. The biggest bother, it seemed to me, was that there were two or three titles no offered by Kobo at all. This will probably be the next frontier of Amazon's fight: publishing exclusives.
Finally, in the realm of Android tablets (I know you're looking at e-ink, I'm just throwing this out there), non-Kindle/non-Nook buyers can always download the store apps which let them read Amazon/B&N books, while store-branded tablet hardware owners are likely to stay in their walled garden without substantial and time-consuming efforts. If fragmentation does occur in the marketplace going forward such that some titles are only available from some stores, you're going to want to look at solutions that let you have access to all your purchases without jumping through hoops.
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