Another wonderful improvement! I'm officially uninstalling my other ebook readers now!
Some suggestions:
1) Differentiate the Quick Highlight icon from the Notes Highlight. Perhaps a different icon, and maybe even change the color of the quick highlight to reflect the color that is set.
2) It is nice in other apps to see 3 or 4 quick highlight colors in the popup bar. So, perhaps the solution to #1 is to simply allow the user to customize which colors show up (either as a colored icon or just a colored circle) in the popup bar. If they want 1, 4 or 8, that's up to them.
3) Allow to click away from the notes editor window and it will save the note and return to text, rather than the intermediate window with all of the arrows.
4) Multi-select and delete in Browse Annotations in the main window
5) Edit annotations in Browse Annotations window
6) Export annotations from Browse Annotations window
Some related suggestions, perhaps out of the scope of this discussion:
7) Allow to search the book for the selected word(s)
8) Allow search of wikipedia for selected word
Here's a couple screenshots from Google Play Books and Kindle for PC for reference regarding many of these suggestions (although I MUCH prefer the minimalism of the Calibre popup bar)