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I'd say that you need to start with what you plan to do with your reader. E-paper devices are really good at reading text based content and pretty poor at doing anything else. If you really want something that will do e-mail, web surfing, movies, and games, then you want a tablet. If you really want something that will provide you a reading experience almost exactly like a book, then you want e-paper. If you want a device that will do both, you're going to be disappointed.
Rooting Android based readers permits book reading apps written for Android to be used on the reader. For instance Cool Reader has some really nice display features that people like. You can install the Amazon app and read books for Kindle on something that's not a Kindle. Understand that rooting is NOT supported by the manufacturer. If you really want to put a Kindle app on your rooted Nook, you better go ask lots of questions in the Nook forum first.
You are correct that if there's no DRM, Calibre can convert from and to a wide variety of formats.
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