I am not sure what the question here actually is -- the title compares apples to oranges (e.g. Obsidian uses YAML for meta-data but markdown is the markup language). Then in the post itself, it sounds like you ask a question about how to organize your note storage. Separate questions with some potential overlap.
A couple of questions -- what didn't you like about Obsidian?
Have you considered Emacs and Org-mode?
A couple of questions -- what didn't you like about Obsidian? Have you considered Emacs and Org-mode?