I'm an admitted matrix fanboy, but i hear ya about organizing in the matrix world! There certainly are opportunities for improvement. That being said, i feel like the challenges are 80% ~ 90% UI/UX challenges that need to be evolved, and maybe 10% ~ 20% protocol/architectural challenges. I have a feeling that there will be improvements from the client/app side that will create a positive jump in experience in the matrix world...of course i am biased. :-)
Discord has a clear segmentation where a "server" (community) has multiple "channels" (and "forums").
I can easily context-switch between servers. With Matrix there is no clear way (at least to me) to get all channels from a specific context - that is provided by someone else. I can of course manually organise channels somehow, but that's not what I want to do.
Example: When I join the Retro Handhelds community[0] on Discord I get access to a huge amount of channels, created by the server admins. I then have a fancy UI (Channels & Roles) where I can pick which specific retro handhelds I am interested in (RG35XX and Anbernic) and it hides the other channels from my view.
There are no other tools that can do this currently. Matrix has the technical capability, but their insistence on making the client NOT-Discord is getting a bit tedious.
I WANT to like Matrix, but they're making it so damn hard.
[0] https://discord.gg/retrohandhelds