I like the addition of different sorting methods: by reference, date added, title, note color.
For highlights, the title is basically the text being highlighted, and sorting by it makes no sense. (it does make some sense for other types of notes)
I initially thought sorting "by title" meant "by title of the resource" This would be very useful, in my opinion. It would allow all the people who are tempted to create a bazillion highlighting notefiles refrain from taxing their system and File menu, that is atrocious as it is. Can you imagine a separate notefile for every resource in your library? How would you ever found a notefile to be opened in this mess unless you typed it's name?