I switched from OneNote to Notion a while a go, one major reason being the possibility to easily export notes in Markdown format. I think it's working pretty well, or am I overlooking something?
Notion's export used to dump it all in one opaque blob of files with no structure aside from some CSV files that roughly described where things went. Maybe they haven't used it since Notion changed it to use folders.
Sounds like org-mode or vim-wiki would be up your alley. This appears to be quite similar but with a modern interface and probably better prebaked configs.
But just keeping folders of Markdown notes is also inflexible, but on the opposite side of the scale.
Obsidian looks like a great balance! I've requested beta access as well.
Edit: Obsidian seems to make it easy to create a Zettelkasten, sort of like https://github.com/alefore/weblog/blob/master/zettelkasten.m... but with automation baked in.