Dr T-- I meant that I only want it to emulate some aspects of paper, but not others. I scribble all over my papers, too, but part of that is because (1) I prefer scribbling to typing, and (2) it synchronizes my notes with the information on the page. What I don't like about it is that a physical page has limited real estate, and there's no reason that my notes need to be bound by that restriction.

I think it could be done in a way that's as unobtrusive as scribbling on the page-- it could be an alternative annotation mode. Currently, the annotation mode interprets any mark on the text as a line. Instead, an alternative default could be to interpret it as highlighting/selection, and bring up a new note.