I think it's great to have the ability to mark up a PDF document within Evernote, but there are some folks who don't like taking notes on the document. It would be incredible to have a capability when viewing a PDF so that a small note section appears below the PDF at the bottom of the screen (think of the notes section in a Microsoft PowerPoint document). With this view, someone could flip through the PDF pages and take bulleted notes in the notes section, without leaving the PDF full-page view. There should also be a toggle that causes the notes section to appear/disappear.
When the user is done reading the PDF, the notes they took would appear directly below the PDF document. This would be a tremendous capability for those who read PDFs frequently.