@stites,
I am no academic or student (anymore), but I use Zotero and .bib, plus I have just written up an article on how to use PDF-Tools, Org-noter, and Org-roam-bibtex together in Emacs on Windows (Org-ref is also part of the overall guide); Zotero is a central part of it, without explicitly mentioned as such (I just assumed it would be for many of the readers of the guide).
… so, I may be able to contribute a perspective.
I would not say “don’t do it”; I am assuming you might feel that it was better if you moved away from Zotero/Mendeley to an “org-based soltion” (?)
I am trying to understand your reasons why you might want that. If you are comparing org-protocol with Zotero/Mendelay, I feel that this comparison may be comparing an apple to an orange (not a valid comparison).
I see the whole “ecosystem” where Zotero (and its plug-ins), Org-based packages in Emacs (e.g. Org-ref, Org-noter, Org-roam, and Org-roam-bibtex) work nicely together, like this in the crude illustration I have just done below…
You have at least 4 “functions” to think about:
- Capture
- Write notes
- Write up [something] – academic paper, blog, etc…
- Manage bibliographic database
To me, org-protocol is (only) one of the tools for capture. Zotero is mainly a bibliographic database, with capture functionality (works on mobile browser, too). I didn’t realise that Org-ref works as a capture tool, too (“grab the bibtex”); I use Zotero for this purpose. Zotero does work well for grabbing / capturing PDF documents for bibliographic database, so that would address one of your pain points (and on mobile browser, too; so maybe two pain points?).
What would be reasons for you to prefer “just an org-based solution” to using different tools such as Zotero / Mendeley?