Considering Matrix age, and precedents, my bets/hopes are for a new protocol to emerge as a “modern Matrix” (just like Matrix was marketing itself as “modern XMPP”).
Matrix just doesn’t have a great and smooth UX right now to compete with the main actors, the heavy protocol is to blame so that’s not something we can hope to see sorted out quickly/on time.
You can see by yourself at https://triliumnotes.org/
It’s FOSS, it’s web so you can use it hosted, or local first as an electron app, or both and then they will sync together.
It is NOT a UI for a folder of markdown files, because that’s silly when you expect from your system to hold relationships, metadata, rich note types, notes to coexist in multiple places, etc. Since it’s FOSS, and since you can sync your notes real-time and distributed across machines, there’s nothing wrong with this.
You can use the web version on Android as a PWA, but it won’t sync offline. There are workarounds to run a local server on your device for that use cases (not ideal in terms of user-friendlyness, but gets the job done).
You don’t need to pay anything to anyone if you host it yourself or if you keep it local. There is no official hosted plan, some people offer to do that for a tiny fee at https://www.pikapods.com/ (never used them, some people say they are decent).
Have a look at Trilium. Anything Obsidian can do, it does better. And syncing is native.
Just making sure you’re up to date with meta+v as clipboard manager (your important stuff in your clipboard isn’t lost)