I have limited experience with different epub formats mainly because they seem to be either limited to a hardware platform as in the case of Kindle or limited in content and clunky to use in the case of e-reader apps. Depends how you define the term epub PDF is already epub in the sense that it not paper-based. The main advantage of formats other than PDF I can think of is dynamic layout and pagination which makes effective use of small screens. However that can be either an advantage or disadvantage in the sense that if the author or publisher wants a distinct house style layout in dynamic layout that may be harder. I suppose highlighting andments can be just as easily implemented with both at least technically.