Good question. I was thinking along those lines, using the note utility on the EE where you type the note, because I figured it would be easier handling the text files.

I have been playing with an open source editor called "Skim" for OS X. It actually works quite well, and gives you many options for export — the whole document or just the notes/comments. For the export of notes you can choose FDF, RTF, Text or their skim file.

So, working in Acrobat, you can export your comments/notes to FDF and then open the FDF with the pdf in Skim. It actually imports all types of the comments from Acrobat, including the scribble notes made with the pencil tool. It even works the other direction quite well (from Skim to Acrobat). A couple of hiccups, but I was quite impressed. That's what gave me the idea to ask for the export feature. If EE were able to do this it should circumvent Adobe's issues with altering ebook/copyright content, and we'd have a way to manage notes when the file is off the EE.

With the pencil tool in Acrobat and Skim, you can attach a comment box with text in it. I was surprised that Skim was able to maintain all of the function. I think with the EE, if they could export the scribble as a vector object (or something) maybe the comment box could be added in the other programs.

Who knows. Maybe there is a way to export attachments as well. Although, Skim doesn't handle them. And it would be very cool to have the EE export the TOC's you create in them (or does it do that already?)