As far as I can tell it is a marketplace issue. If you are selling your books and need to be on the major platforms like apple's ibooks and itunes, amazon etc. you need to be formatting to the e-readers like epub as they don't accept PDF. If you don't need to be on these platforms then PDF is fine. It's a shame it has to be so convoluted. As a publisher that does graphics-intensive and large page count books we have been waiting for epub3 to get its act together. Hopefully a standard will emerge because as it is now, it's a hot mess for designers.