Not all eBook readers are the same and if one creates an eBook using InDesign it gives you a lot more flexibility with regards to what you can do with the formatting of the final file. At this juncture, Amazon has made pdfs more user friendly insofar as pdfs can be converted and will allow text reflow, but beware, only books with straight text and without headers are the only ones that will really work well. Recently we did a test on a book that was not straight prose. The result really had to be seen. Charts didn’t come out correctly, page numbers wound up showing up oddly, in some cases two separate page numbers at once. Some text was capitalized and not capitalized in the same word. Photos wound up with the corresponding text in the wrong location. In short, it was a complete mess. If you want to test what your pdf will look like as an eBook, download Calibre, convert your file and see if you like it. That’s not to say that things won’t change and one day pdfs will be usable, it’s just not now.