The main annoyance is that some of the settings are global. I usually have many PDFs open at the same time and you can't hide the sidebar / show chapters for just one PDF, it always changes for all of them. Also there are not tabs. There is no easy way to jump back and forth between two pages that might be far apart. And I wish I could peek links to other places in the same PDF.

I’m also curious to know. Preview is pretty much the only tool I really miss whenever a switch from Mac to Linux for a while, and it works really well for annotating and basic editing (moving pages around)…

It randomly deletes all of the comments in the file. I had this happen at least four times. Preview overwrote the file, deleted all of my comments, which were at least a couple of hours of work.