It's missing collaboration at the core, although it's possible to achieve this currnetly with third party solutions, or the next major update should also include it as it's the "multiplayer" update.
We have a novel architecture where you can optionally register a self-hosted relay server with our control plane for complete privacy for all of your docs and attachments.
We know that people typically prefer to have a unified vault, so you can share individual folders with different groups of people within your vault.
Relay is free for markdown docs up to 3 users, and then we have a hobby plan which includes attachment storage (especially popular with D&D and TTRPG players), as well as per-seat plans for businesses and universities. There are a couple of cloud-only alternatives like peerdraft and screen garden as well.
[0] https://relay.md
I don't use the 'linking' feature between notes. The whole 'second brain' thing seems like something you do to make a neat screenshot of your note graph. I just use regular old folders like a file directory. My notes have gotten a little messy though.
Transclusions (embeds) are very useful also.
I agree that the note graph visualizer is just a gimmick though.