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I have both, and rooted the Nook. Thoughts:
1. Form factor isn't really important. Both use the same touchscreen technology. The Nook also has turn buttons, but it is difficult to press them.
2. Rooted, Nook is great. Running six different reading apps and six different publication apps (like NYT). But it takes some time and configuration.
3. Out of the box, Kindle is better for a couple of reasons. First, sound and TTS. Sounds silly but try listening to the lady when your eyes are tired. You can catch up on an article or chapter in the dark. Second, nothing beats Send to Kindle, both from Calibre and from various web apps. This makes the Kindle truly wireless. The best I can figure out to do this with the Nook is through Dropbox, but it is clunkier.
4. Rooted Nook has better games, there are plenty of puzzle and word games in Android that play nice in monocrome. Kindle also has some ok games, though.
5. Unless you hack the fonts, make sure you like the stock font with Kindle. I didn't and replaced it, but it took some jiggering. Nook has multiple stock fonts, then even more if you root and use another reader program.
So I'm ending up using my Kindle on the road and in bed, and my Nook as a monochrome tab.
Buy both and return is pretty good advice, although you may have trouble returning a rooted Nook.
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