On a broader protocol level, it's just a case of "unexpected moderation pitfalls". Matrix is far more decentralized than even something like the fediverse is, which comes with a couple of issues for public servers. They're not really technical issues but social ones.
If we get down to brass tacks: things like how it's technically impossible to forcibly disband a room unless all parties agree to it/are manually kicked beforehand jump to mind as an issue that's not fundamentally broken per-se but is an example of "wait, that is supposed to work like that?".
Other than that, multi-room moderation is a total crapshoot. I've tried it, it just was a mess. You end up trying to plug in a moderation bot like Mjolnir onto your server and need to do the moderation through it instead of native clients. With the most common model for chats nowadays being closer to the discord model (where a subject might have many channels as opposed to the 2 or 3 you get on IRC), this isn't really workable.
Generally speaking, matrix doesn't seem to like many channel setups very well - there's been two attempts so far from what I can tell to solve it, but both just result in attempting to bolt existing channels into a "discord guild"-esque system with optional joining like it's an IRC channel list, which isn't how most people expect that to work. This is mostly a UX thing though - I imagine someone could write a client that just assumes the solutions on this in a better way.
The rest of it just amounts to some variant on "Element sucks" (which since it's the "main" client, makes it the most used one). The easiest example I can think of is that you need to use a GitHub PWA or send manual curl commands to say, set a server ACL on a channel or take server moderation actions on one of your users is absurd/unacceptable if you want to run a public service.
The main reason I call it fundamentally broken is because a lot of these issues seem to have been there for several years and the priority doesn't quite seem there to make the experience of using Matrix easier. Element lacking good moderation components for example is something I've noticed for years on end and updates never seem focused on improving any of it.
Sorry if this is all a bit disparate in terms of complaints/haphazard complaining about Element - they mostly come from running Synapse since ~2019 (+Element, back when it was still Riot) and in my experience updates to it never seem to have addressed many of the pitfalls/unexpected behavior that Matrix runs into compared to other chat apps I've used over the years.
If we get down to brass tacks: things like how it's technically impossible to forcibly disband a room unless all parties agree to it/are manually kicked beforehand jump to mind as an issue that's not fundamentally broken per-se but is an example of "wait, that is supposed to work like that?".
Other than that, multi-room moderation is a total crapshoot. I've tried it, it just was a mess. You end up trying to plug in a moderation bot like Mjolnir onto your server and need to do the moderation through it instead of native clients. With the most common model for chats nowadays being closer to the discord model (where a subject might have many channels as opposed to the 2 or 3 you get on IRC), this isn't really workable.
Generally speaking, matrix doesn't seem to like many channel setups very well - there's been two attempts so far from what I can tell to solve it, but both just result in attempting to bolt existing channels into a "discord guild"-esque system with optional joining like it's an IRC channel list, which isn't how most people expect that to work. This is mostly a UX thing though - I imagine someone could write a client that just assumes the solutions on this in a better way.
The rest of it just amounts to some variant on "Element sucks" (which since it's the "main" client, makes it the most used one). The easiest example I can think of is that you need to use a GitHub PWA or send manual curl commands to say, set a server ACL on a channel or take server moderation actions on one of your users is absurd/unacceptable if you want to run a public service.
The main reason I call it fundamentally broken is because a lot of these issues seem to have been there for several years and the priority doesn't quite seem there to make the experience of using Matrix easier. Element lacking good moderation components for example is something I've noticed for years on end and updates never seem focused on improving any of it.
Sorry if this is all a bit disparate in terms of complaints/haphazard complaining about Element - they mostly come from running Synapse since ~2019 (+Element, back when it was still Riot) and in my experience updates to it never seem to have addressed many of the pitfalls/unexpected behavior that Matrix runs into compared to other chat apps I've used over the years.