Yes indeed the use of a PDF lecture note feature is a specialized feature, for serious note takers, which most students are. I take notes at about 8-10 lectures per week, and I guess other students at various levels take notes at lectures quite frequently too :-) I attached a screenshot from OneNote, which has an excellent layout for note taking in PDFs, BUT IT IS USELESS since it takes from 18 hours to 3 days to sync one single note.... not great. Evernote is still the best at taking notes from scratch on an empty page, and great to draw directly into the note with Apple pencil on the iPad Pro.
Here's a feature I think would be super useful for all students (myself included), a way to handle PDF slides in evernote, in addition to the normal Skitch annotation. An option to import PDF files (i.e. lecture notes) to a new note, and each slide would appear in the notes window, directly ready to annotate. And each slide would have an "own notes" section directly on the side of that particular slide. No application has a workable feature like this (OneNote has one but it doesn't work well). Please for the sake of all students, consider developing this kind of function to work on Mac and iPad Pro (with the Apple Pencil).