[Dylrob]

Notability is more of a note taking app. A very powerful one actually. I use it all the time in my classes because it can can voice notes and sync to the written/typed ones. I sometimes use it for PDFs, however keep in mind that it has to import the PDF into its native note format first. (you can export it back into a PDF, but I imagine you’ll lose certain things like TOC)

GoodReader has been my go to PDF app since I first bought a generation one iPad. It's basically a advanced file manager with PDF functionality on top of it. TBH though, while it was vital to me in the early days, as iOS’s file management has improved in recent years, I find this program to be increasingly cumbersome. If I could find another program that lets me crop out the margins in the same way this one does, I’d probably switch.

Now as for a simple PDF editor, the native Files app technically qualifies. You can very easily make highlights, comments, and hand-written notes. The only major downside to the Files app is that it doesn’t have any way to bookmark or remember the last page you were on.