Kindle will have biggest book selection, ESPECIALLY non-fiction, text book types.
The ability to just email a document or pdf is incredibly useful on the Kindle, too. I've used both for school and the Kindle was a HUGE improvement in terms of how much time I spent messing with files.
Still, PDF support isn't GREAT with the Kindle - though it is pretty solid. The Sony reader can flow text in a PDF so it works quite well for that.
But I do use my Kindle for the same reasons you mentioned (and the Sony) and I'm happy with the results 99% of the time.
The bane of my existence is two column pdfs. I don't know if the Sony can do any better with them, either.
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