It would be nice to have the option to display the notes you've made along a right-hand column in the resource. In other words, it would be laid out like a Study Bible, except instead of all the notes being at the bottom of the page, they would be along the margin. (Similar to how a comment is appended in Microsoft Word.)
How would the program handle notes which expanded beyond the space of the original text? Same as Microsoft Word handles comments, which is somewhat similar to the way note-tiles are handled on the left-hand pane of the Logos Notes tool.
Allow users to choose which notes are displayed in margins, integrating with the current icon layout. Perhaps it doesn't have to be fine-grained, choosing individual notes to display in the margins, but it can act like a visual filter where *notebooks* can be displayed or collapsed into the current icon layout.