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I wouldn't even recommend the nook without rooting the device. I had the stock nook for a few days and was underwelmed by the device. However after rooting the device offers so much more.
As for annotating, the sony device is still the best for freestyle writting. The kindle and book color do a great job at annotatinpd their formats. The kindle is better than the nook for pdf. The kindle has full support for pdf the book only reads pdf.
As for notetaking in class. The android platform has a slew of good office apps. Qickoffice, thinkoffice, and documents to go come to mind. There is even gdocs.
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