The problem is that PDF is a terrible format for eBooks - that's not what it was designed for, and not what it's good for.
The fundamental issue is that a PDF file is formatted for a specific page size, and (unlike "real" eBook formats) cannot "reflow" to accommodate other page sizes. An A4 PDF is "stuck" at A4, and can only sensibly be viewed on an A4 screen (or printed, which is what the format was originally intended to be used for, of course).
To view a PDF on a small screen, such as the Sony Reader, or CyBook, you have only two choices: shrink the PDF page to fit the screen of the device, or provide a way of "panning" a viewing window over the PDF page. Neither of these provides a very satisfactory experience.
What formats are better? Practically everything, to be honest. MobiPocket on the CyBook or LRF on the Sony Reader, to name but two.
Anything is better than PDF as an eBook format.
There is, I should add, a recent variant of PDF which allows pages to reflow, but very few portable devices support it, and even fewer PDF documents support reflow.
If you
create a PDF specifically for the page size of the reader, that's a different matter, and works very well indeed (this is what the
Feedbooks web site does, for example). The problem occurs when you try to view A4 or US Letter PDFs on a device such as the Reader or the CyBook, which have only 1/6th the screen area that the document was designed to be viewed with.