You mention PDFs. Remember when somebody suggested using them almost 20 years ago!
Current status of PDFs is that Adobe has adding a "reflow" bit to the standard in recognition that people reading documents on electronic devices NOT paper want to be able to read those documents in sizes appropriate to display on those devices. Problem is that the reflow bit doesn't work with many common PDF layout techniques that overlay text on graphic elements, or on layout techniques that combine graphic elements with textual elements. Now some "PDF" devices ignore the reflow bit and reflow PDF documents "without permission" and other "PDF" devices ignore the reflow bit and never reflow the document even if it would be appropriate to do so on that device.... In summary: given the presence of "reflow" or the need to perform reflow because different display devices can be much larger or much smaller than a standard sheet of paper, the problems of the new improved "PDF" file format essentially become identical to the problems one is always already running into using HTML, MOBI, and EPUB file formats.