My honest solution is “atomic folders”, which you can see here:
I don’t do much linking, but I make good use of the vault search tool. I don’t try to pre-design my workflow anymore, except for trying to maintain simplicity and brevity (i.e., non-complex templates). I have been waiting for the “metadata improvements” from dev team for a while now which means I have not used metadata at all (dataview or YAML) because I want to see what capabilities will be added first. Not using metadata has been quite freeing.