I see that better margin notes made it onto the Google summer of code for OOo.
here’s a totally unusable little chunk of experimentation around notes which might help someone interested in this to see some of the classes that interact in this area and the sort of things that might be useful in properly implementing this.
I suggest doing it just for “normal” view, and leaving things as they are for “web layout” view. Expanding the right margin area to make room for the notes, and then using either writer frames or MultiLineEdits to implement the notes themselves, select a better yellow for the margin notes background and draw lines across the page from the margin note anchor position to the margin note, and then layout the margin notes as close to horizontal across from their anchor postion as possible, pushing them out around the anchor point into the available space if notes overlap.