Many thanks, @Kabo, for this compilation and the wish list. This also helps me trying to develop an independent third-party solution which has many similar goals. There are many individual efforts happening redundantly…
Ideally, we’d have a common (i.e. widely accepted & usable) exchange format for annotation and reference data. The latter has at least some (not really standardized but common) formats (like BibTeX, or even better, Citeproc/CSL JSON).
Then there could be a tool solely dedicated to converting these data into desired output formats using a common template syntax. There could be a public repository of templates where templates could be shared easily.
When I started my own endeavours years ago, I tried to get people on board to agree on a common plaintext/Markdown format for annotation notes. That never worked out since, as you noted above, individual needs are way to different. But common data formats together with a common templating syntax may be (slightly) more realistic.