I’ve been a very happy user of LiquidText [1]. You can load multiple PDFs/images/documents into a LiquidText project and annotate and cross reference. There’s a separate work space outside of the documents where you can store clippings and collect summaries.

It’s great for reading long standard documents and cross reference between them and supporting material like examples etc.

[1]: https://www.liquidtext.net/

I've gone back and forth between Apple Books and Acrobat Reader a lot.

Ultimately I currently use Books because I do a lot of multicolored highlighting which is far more consistent in Books, and because Books lets you set bookmarks (to go back and forth between main text and endnotes) which Acrobat inexplicably still does not support.

Ultimately every PDF app is good at some things and terrible at others, and you're just going to have to find the app that has the best set of features for you. It is pretty sad that all the apps have significant drawbacks for certain common workflows.

I like GoodReader for this. It’s the only app I’ve found that stores my annotations in the PDF files themselves, and allows me to keep my PDF library in sync over SFTP, Dropbox, etc. so that I can read and annotate documents on non-Apple devices as well.

On the iPad, I use goodnotes for that. You can import PDFs and then mark them up.

PDF Viewer has worked well for me, personally.

I use notability on the 12.9 inch iPad Pro. You can import the pdf, then annotate