PDF works absolutely fine for the Kindle and nook, provided that it's correctly sized for the 6" screen. The issue arises when people try to read PDFs formatted for an A4/Letter page on a 6" screen - that doesn't work at all well. If the PDF is designed for the 6" screen, it will look good. The issue with PDF on the Kindle is that hyperlinks don't work, dictionary lookup doesn't work, and you can't add annotations.
But I'm a little puzzled by your mention of the Kindle. Weren't we discussing an ePub book? The Kindle doesn't use ePub.
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