After three years with Obsidian and Zettelkasten, I have three constraints I cannot organize my way around.
Publishing is a separate workflow
Obsidian is useful for collecting source notes, linking ideas, and drafting. It is not my final environment for academic work: citations, footnotes, and export to a required format still need too much manual cleanup. I now move a finished long-form draft to Overleaf or Google Docs instead of trying to make the vault do both jobs.
Structure does not maintain itself
Maps of content become hard to use when too many notes qualify, templates drift, and definitions get buried. I am keeping MOCs for real navigational hubs, and I will write only what I understand while leaving links and practice tasks for the gaps.
Notes do not become action by default
The personal vault is easy to treat as an archive. A useful note needs an explicit next action, routine, or external practice; otherwise it is only a record that I had the thought.