The biggest suggestion I have for highlights is I would love to have my highlights of Bible verses common across all of my Bibles, including original languages. So, if I have underlined Jn 3:16 in my KJV, it is underlined in my Nestle Aland, and my ESV. Just like with paper, I always hated changing Bibles from the old to the new because I lost my notes. Currently, if I highlight something in the ESV, I spend the time to open the KJV and even the Nestle Aland or the BHS.
The same thing could be said for notes. I understand that we may not want a note to be on everything, there could be a toggle for that.
Wilson Hines
Logos 6, user since 1995