Allow notes to be grouped into notebooks (like Microsoft OneNote).
I would find this so much easier because I have many notefiles for different things and it gets messy.
Mark Chenhalls commented
Amen - Logos support indicated that performance of the application is greatest when each resource has its own separate Notes document. Since I highlight / annotate in many different documents, then this results in a huge list to search through. A folder grouping would facilitate finding the notes file rather than remembering the exact alphabetical title of the resource in which the annotation was created