Apple - What readers annotate PDFs better than the Preview app?
Skim is a pdf reader specialy designed to annotate pdf.
Skim is a PDF reader and note-taker for OS X. It is designed to help you read and annotate scientific papers in PDF, but is also great for viewing any PDF file. Stop printing and start skimming. Explore the links to the left to investigate Skim and consider helping out with the project.
Features:
- Viewing PDFs
- Adding and editing notes
- Highlighting important text, including one-swipe highlight modes
- Making "snapshots" for easy reference
- Navigation using table of contents or thumbnails, with visual history
- View all your notes and highlights
- Convenient reading in full screen
- Giving powerful presentations, with built-in transitions
- Handy preview of internal links
- Focus using a reading bar
- Magnification tool
- Smart cropping tools
- Extensive AppleScript support
- Bookmarks
- Saving passwords in Keychain
- Export notes as text
- Automatic download of remote PDFs
- Support for Apple Remote Control
- Interaction with LaTeX, SyncTeX, and PDFSync
- Integration with BibDesk and other third party applications
- Spotlight support
- Highly customizable
- And much more...
PDF Expert is hands down the best pdf editor made. Better than Acrobat.
While not meant primarily for your use case, I found Mendeley Desktop to be quite adept at highlighting and annotating.