I know what your question was
but the kind of books is not that unimportant for the choice of the right format.
- pdf is a static format. Most of the files are edited for "big" pages like A4 or Letter size and not for 6" readers. In this case it is very hard or impossible to read them on a kindle.
- mobi/prc is a reflowable format. The user itself can change the font and font size. You as a developer can't always know on which device your book will be read. Mobi files work fine on small phones, on 5" or 6" or 10" readers or on PC screens as they adjust themselves to the screensize.
- I don't know how the kindle handles this, but on a Cybook Gen3 (another reader capable of reading mobi files) you can only look up words in a dictionary in mobi files but not in pdf files.
- If you develop your files exactly for the size of a 6" device or if a certain layout (say a certain font or pictures embedded in the middle of a paragraph with flowing text around) is important than pdf files will work fine.