My e-reader reads PDFs relatively well; It just doesn't support changing the font size, making it a bit harder to read than EPUB. Maybe it's a limitation of PDF, not this reader particularly.
So it looks like, because of the nature of PDF, Calibre and other tools simply cannot handle more complex parts such as tables or insets.
Incidently, considering how many e-reader users need to access PDFs, I might not be the only person curious to know more about PDF without delving too deeply either, and understand how it works (Postscript, etc.) under the hood and why it's such a pain to turn into EPUB.
Are there other sites/books you would recommend?