Something that I've always thought might be a good idea would be to have the option of adding author's notes as a separate "page" to a chapter.

I see it as being an option inside the story manager / chapter manager section. Add it, and a text field, below the chapter title box. The author can then add in the author's note which could then be viewed as a collapsible header/footer on that chapter's page.

This system would hopefully work to eliminate long author's notes that we're just scrolling past anyway; if someone wants to read the note it gives them the option, but the rest of us don't have to. Also, since the notes would no longer be part of the chapter the word count for the fic would be far more accurate. No more padding a chapter's word count with 3k of A/N to fake people out.

Just a thought.