I would say the new Kindle is a good choice. She already uses Calibre, so she shouldn't have much of a problem with converting. It depends, if she wants library books, some don't offer mobi format.
I use calibre and it works well with the Nook. I have it rooted though (which is pretty simple), and if I didn't I probably would have went with the Kindle 3. If it's not rooted it doesn't have very good organization. When rooted you can set the Nook up (via tags in Calibre) similar to the collections on a Kindle. The thing about the kindle (besides amazon and DRM) that I didn't like was that it didn't show my book covers until I opened the book. I know it doesn't seem like a big deal, but sometimes I remember the cover and know I wanted to read it because of reviews or recommendations, but can't remember the title. The battery life on the new Kindle will be much better than the Nook. I have had my Nook for 4 days and I am at 50% battery life (I have played with it extensively though). If she lives near a Barnes & Noble she can go into the store and read any book for free for an hour.
Kobo works well with calibre as far as I know. It is small and light. It is a lot slower though, and the screen isn't quite as nice as the Kindle or Nook.
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