Notes-only display
Would it be possible to have an option to show all notes (both standalone and those attached to sources) as a single flat list in the middle pane? Once I've read and made notes on a number of sources, it'd be useful for me to be able to see all the notes together so I can begin to synthesise them.
However, you can now create a report that consists only of notes. Create a saved search for "item type" [is] "note." (The saved search will display linked sources as grayed-out items.) Then right-click/control-click on the saved search in the left pane and select "Generate Report from Saved Search."