I'm in pretty much the same situation. My thread, "Thinking out loud," is a few down from this one. I'm leaning toward the Kindle 2, not because I think it's ideal for academic work by any means, but because the various trade-offs seem to point in its direction. From what I've seen, the content on Amazon really is cheaper than most of its rivals (I don't know that you're in the US, which is a factor), and there's more of it, particularly in non-fiction. Whether your academic field is well-represented in Kindle is another question. In mine (philosophy) it's mediocre, but seemingly better than the competition. And since academic publishers are dealing in lower volume, I'd expect them to be even more interested in Kindle's (or somebody's) DRM scheme, as time goes on. But that's just a guess.
Like you, I want to be able to annotate, or at least highlight.
I'm also considering just waiting a while. I don't have an iPhone or iTouch, or any plans to get one. I do have a Blackberry Curve, with Barnes & Noble's eReader on it. I've been doing some reading on it, and it's not nearly as bad as I expected it to be. I keep the type size jacked up to about 40 pixels, which is larger than most book fonts, and even though the lines are necessarily short, I don't seem to experience much eyestrain. I keep the backlighting at 50%. I'm actually tempted to swap the Curve for a Storm, which has a larger screen, if I use it in landscape mode. In addition to the B&N reader, Mobipocket is available for the Blackberry. And the cost, taking into consideration the sale of my Curve, would be less. Obviously, this won't be the way to go for the academic stuff, for the most part, but for other reading, maybe.
So, I'm still undecided about whether to spring for the Kindle 2 or just get a Storm and wait to see what comes along in a few months or a year.
Todd
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