I happen to have an iPad Air with an Apple Pencil but I didn’t find a good app for annotating pdfs. I always end up zooming in a lot, writing notes and zooming out. Again, this breaks my flow.
I saw the Remarkable2 which may be good for my purposes, but I’m interested in hearing other solutions
GoodReader has better file organization capabilities.
GoodNotes has better annotation capabilities.
Both are cheap.
A 12.9" iPad isn't cheap, but it means you don't usually have to zoom.
If you can stand subscriptions: also Notability.