PDF is not an eBook format. It is a digital representation of a printed page, with a fixed layout. It is not possible, for example, to create a PDF for a Kindle DX with a 9.7" screen that will also look good on a Kindle 3 with a 6" screen.
PDF is an excellent format for its purpose, but that purpose is not to create eBooks.
Currently proofreading The Poison Belt, by Sir Arthur Conan Doyle.