The problem is that since OneNote backs everything up, and the way it stores PDFs and such is as really large image files You can annotate the PDF and export the annotated version, but you can also bring out parts of the PDF (text, or graphical portions), linking into the place where they were taken from in the PDF, into an infinite canvas where you can freely draw, hand write or type OneNote actually does pretty well for handwritten notes in my own opinion. Play with pen colors and thicknesses