Pros of working with PDF
Ability to use output from other layout applications such as QuarkXPress. Simpler preparation especially for older backlist books, no need to find all links or to activate fonts, simple tools to quickly build pages, embedded text for search is available. Hyperlinks can be retrieved with CircularFLO tools.
Cons of working with PDF
Live selectable text will not be available, harder to add animation and other interactions to parts of the page.