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What made the difference for me is the way Amazon and it's devices handle highlights and notes. Having all highlights exported to its website where you can see them and cut and paste is just way to handy not to mention that my nook and nook apps don't also sync to the last page read as well as they should. Since I read on a multitude of different devices those two features were a deal breaker.
9 months ago on Kindle vs. Nook