Mostly to do with the permissions system. I want a hierarchical set of categories and channels, and I want to be able to set one user as a privileged user, and instantly get access to all of those channels, or some of them, depending on the permissions settings. I also want some users to be able to see some channels, but not all, with only a single join action. In discord you join the "server" and you get all channels unless permissions specify otherwise. Then when you get a role, you may be able to instantly see and use several other channels. Some servers let you choose your own roles, and manually give you others, to customize what you can see and interact with.

With matrix there are... permissions. But they can't be inherited by a room from some sort of category, it's hard or impossible to automatically hide some rooms from users who join a space, with an option to instantly give them access to those rooms with an easily configurable toggle. Rooms tend to act like their own space sometimes, and each can have their own invite which is annoying. I want them to act as a collection under a single membership, just like you can join a single discord server, and whether or not you see them, all channels are contained in that server and getting access to those channels is a matter of role permissions. I also vaguely remember having trouble with the admin stuff and adding other admins/moderators to my matrix space, but I can't remember what problems I had with that.

Basically it's hard to make a large matrix space with many many rooms that have different purposes. Not to mention the lack of forum channels, those are required for my type of large community.

I have a few hundred people in my community. I imagine it's much worse with larger communities.

Edit: now that I think about it, my moderator team even looked up some of the missing features, and the matrix devs had stated that they are not planned, and that is not the direction they want to take matrix in. Which is fine, but that means it has a completely different use case than something like discord for communities.