Old topic, but, there is a easy solution
I know it's an old topic, the OP has sold his ipaddle, but for anyone who is interrested: PDF Expert is the app that exports your highlights in a book (pdf only) to a pure text-file, which can be synced through iTunes back to your PC.
I use GoodReader as my primary pdf reading tool, and hightlight / annotate heavily. When I'm done with the book, I send it through the GoodReader file manager (Select the book, Open in..) to PDF Expert, where I save the annotations only in the txt file.
Have searched a couple of weeks to get to this, so I must agree with the OP about the fact that this (for me anyway) BASIC feature on Windows and Android is so rare in the ipad world. Don't you find occasionaly stuff in a book that you would like to remember and find noteworthy? Is it possible that only one person in the forum mentioned this before as someone in this thread mentioned?