Emacs org-mode is better than Markdown.
+1 for Emacs Org-Mode.
But of course you'd have to have bought into the Emacs ecosystem. Then again, Org-Mode may be a good first step!
Evil mode makes org-mode very approachable for anyone familiar with vim. Grab doom emacs or spacemacs if you want it to just work.
Also, Elegant[1] is an attractive and simple config. It would probably be worth packaging it or something very similar up with CUA bindings and marketing it as just a standalone notetaking app with Emacs just being an implementation detail.