But let’s go;
1. The note stream panel shows highlighted text with a color line next to the right side and the added note on a full-color background. I think the intuitive interface would turn this around so the highlight would be on a full-color background while the note would be indented with a side line. Perhaps a yellow sideline as the notes are all yellow once closed.
2. I wish the note font size would be bigger or adjustable.
3. I wish we had a simple pen to scribble stuff on the PDFs in order to make it more messy

Those are just little wishes, nothing major

Cheers, Rene