The navigation problems were things like this...
You are halfway through reading a text book and go to read a footnote which is located at the end of the Kindle book since there is no concept of pages. Switch the device off. Next time you switch on, you are at the end of the book. How do you quickly get back to where you were?
You are currently reading 4 or 5 books. Kindle remembers where you are in the most recent one you opened. How do you easily keep track of where you were in the other books?
You have a large collection of books. How do you organise your collection sensibly, and find things easily?
I think the PDF problem was that you have to zoom and pan a lot. It would be nice if the content could somehow reformat for the small screen, automatically adjusting to the orientation of it. It would fit the width, and you'd just have to scroll vertically.