I prefer EPUB, or HTML, format over PDF. PDF has many advantages, but... frankly, it sucks. PDF is designed to replicate, page-for-page, whatever document / design you want. All the 'features' of an image file, without the excessive size.
What it doesn't handle is reformatting to fit the device you use. It's designed to take a document and put it on screen without any changes, or to print it and know exactly what will print with ease.
No thank you.
Anyway, just as a plug, I'm actually planning to provide E-Book, HTML, .doc, and probably a few more formats to my readers once I've finished cleaning up Guardian. (So close... just a few chapters left, and then doing all the final formatting, all too much of which is format-specific).