The nook and kindle both have their plusses and minuses. The nook is a more open device in that it reads epub format and you can buy/find books for it at multiple sites, as well as borrow books from the library. By comparison, the kindle is a more "closed" device because it does not support the epub format. To some people, this will matter. To others, it won't. I have found that Amazon has more of the kinds of books I am buying, so that is not particularly an issue for me.
However, it is only after owning an ereader for a while that you begin to REALLY know what features are important to you. You might think that a particular feature of one ereader is valuable, but then you find after owning it a while that this feature really doesn't matter in your day to day use. That is pretty much what I found with the nook, but that is not a reflection on the nook - only one person's usage pattern of these devices.
For PDF, I think the kindle is better all around, so you should probably try it first. Also, there is a 30 day return policy on the kindle, where the nook only has 14 days. So for that reason, getting the kindle and learning your way around ereaders before making a final decision might be a good idea. You can certainly try both in stores (i.e. Best Buy for nook and kindle, Target for kindle, and Barnes and Noble for nook).
Best of luck...
Tony
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