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You don't say where you're located or if you travel for business. Given your reading needs, I'd say those are important considerations. If you travel internationally, or are located outside the US, then the Nook is going to be a less satisfactory solution since B&N is simply not supporting it outside the US. (Yes, there are workarounds. No, I don't think they are a great solution.)
Given that you found the books you wanted more on Amazon than B&N, I'd go with the Kindle. You can highlight, annotate and mark up your books easily, and those markups, etc., are available on your PC/Mac using the Kindle for PC(or Mac) application, allowing you to easily move them to a secondary document.
Using a keypad rather than a touch screen is not something I think you'll long find an issue. Personally, I prefer it, but others seem to love touch screens. IAC, both work acceptably for what you want to do, and I think you'll adapt to either.
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