Do you have cite as you wrote functionality implemented ? Current research paper tools like Zotero do fine for the organisation and management part. The major limitations are poor integration with text editors and word processors.
In my opinion, the needs of STEM researchers are very different from those of the humanities. STEM researcher tend to use citations to substantiate pre-existing information, almost never have footnotes, and typically have schematics/flowcharts/graphs in their documents.
A good editor should be able to cross-reference citations, figures, handle SVG smoothly and definitely have Mermaid/MathJax support.