On the topic of notes, the firm I am presently employed by is also seeking a slightly more "Photoshop-esque" method of displaying notes within documents. Perhaps even more along the lines of the way Word does things, where text regions can be selected as zone which the note refers to.
My personal preference would be a hybrid of the two. The Photoshop style of handling notes (lets also include Acrobat into this, too, since it shares the basic style), very similar to PostIt notes in form and function, is incredibly user friendly and easy to interpret.
Moving items onto a secondary layer could certainly be done, but problems can occur when the text it refers to moves beneath it, causing a logical disconnect. (Hell, in the later pages of our documents, a change of a few lines early on can result in as much as a three page increase with the compounded content rollovers from large images and such.
The Word method is what was used prior the switch to inDesign, with content markup being handled with bubbles (of sorts) off to the side of the document. While this obviously does not transfer completely into our beloved layout application, aspects of it could be carried over in a way that could function.
If the idea gets refined any further, I'm likely to post it to the CS3 wish list forum.