Why hasn't someone created a program to cut out all those middle steps? Is it a proprietary format issue?
Apparently calibre has such a plug in, but I've not really played with that much.
Kindle publishing is still a bit of a muddle; there are several steps through which you must trudge before you have something suitable for upload. E-book readers are essentially web browsers, and the .pub and .mobi files are web pages with some header information. However, the HTML output is somewhat rudimentary - think browsing circa 1998 or thereabouts, and this is where the problem with direct conversion starts. Most PDFs have formatting that a Kindle couldn't handle well and image placement causes no end of trouble. Also remember that a Kindle is limited to the half a dozen or so fonts it has installed (last year I took a Kindle publishing course where the instructor spent half an hour talking about choosing the right font - a completely useless endevour. I managed to bite my lip through that one...)
So, the bottom line is that you have to strip out all the formatting, and then redo it all and create a TOC (all Kindle books need one to be accepted). Then you compile, test it on all the different flavours of Kindle using the previewer, and finally compile to .mobi and upload.
Do you think I should write something to do all that automatically? It would take all the fun out of it...