I used to do this but I've tried to move to exclusively digital. I always, after some period of time, end up throwing out the papers I've printed. Plus digital allows for easier access across devices, quick searches, etc. Still though, I enjoy reading printed papers more.
Curious if anyone else has a similar experience with print vs digital.
One of the most obvious benefits to paper that comes to mind is the ability to lay multiple non-sequential pages (from the same paper and from other papers) side-by-side. That spatial aspect isn't replicable afaict and I definitely feel like it limits me in many ways.
It takes extra time, and might feel wasteful, but I usually do it some days/week after I read the paper, for a spaced repetition purpose too.
Instead of highlighting I take notes. I write down a list of key points, and I write down a list of topics I'm not as familiar I'd like to be with, including breaking expectations.
I go further and I google around investigating this list learning more on the topics beyond what the paper has to say.
This style may or may not be ideal for you, but it works well for me. Highlighting has always, for me, been not very helpful when compared to taking notes and getting a more solid understanding by combining sources of information on the topic when possible.
My current thoughts are to move more to Zotero because it also has some annotation functionality, but primarily use it as an extraction point to then store these annotations/notes in plain text or markdown. Which then I'll manage with git or something.
I've personally realized it's more important to me to have my notes about the papers easily accessible (hence plain text in git) than to have PDF annotations stored in an app alongside the PDF. I've also realized this has been a little bit of a shift in how I read, making me more focused on extracting information. Not sure how I feel about this yet.