I recently discovered ZoomNotes ($7.99 in the app store; single lifetime purchase). This video from Paperless X on YouTube quickly demonstrates how powerfully ZoomNotes let’s you handle and annotate PDFs. (Heart-eyed emoji in original.)
the BEST PDF-reader for the iPad | ZoomNotes - YouTube
The ability to create links between pages in a PDF is HUGE by itself.
It does have a learning/set up curve because it is capable of doing so much more than GoodNotes. In addition to the features mentioned in the video, you can rearrange and add pages to PDFs and export them back to PDF. Many other helpful videos on Paperless X as well. Current version is 8.6 and the developer pays attention.