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Someone can correct me if I'm wrong, but as long as the book has DRM protection (bought on Amazon or B&N) I do not think you can play with metadata. You need to break the DRM 1st and later, play with it, with Calibre, for example.
Yes, MOBI books have metadata, like ePub.
In terms of PDF, that's not an ebook format. So it will be a hit or miss, depending of the book itself, not the reader. But I do like Kindle better, at least Kindle keyboard or the new Kindle wifi; you have landscape, so it is easier to read some PDFs that way. But for a better experience, I usually recommend a 10" inch tablet. But it is doable on 6" screen.
Not sure about the "series" question, I usually do not read novels, but non fiction ;-) ...
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