This is working great so far. One thing that I ran into that you may or may not be able to fix:
I have a PDF that I marked up with Readdle's PDF Expert (Version 4.7, an old one since I have a 1st generation iPad). The notations show up, but instead of showing the content of the actual notes, they just show as 'Text Highlight'. Also, notes are not shown in the sidebar, but if I click on a highlight that I'd attached a note to in PDF Expert, it does pop up.
Here's an image: http://imgur.com/kYlKXTT
But, neither Papers nor Mendeley properly import the highlights/notes from PDF Expert either, so it may be a problem on PDF Expert's side.
So, this may not be something you can address at all, but I thought I'd throw it out there.