The main ones are that certain users or groups of users end up dominating each community, and that mods become abusive over time. Brigading and bigotry are big issues too. You also mentioned echo chambers, which I agree is another issue, although that is present in many social media platforms.
Unfortunately, federation doesn't solve these issues. At the very least, some kind of basic improvements are needed. Ideas like preventing large communities from dominating the front page, removing or limiting the effect of downvotes, or having more checks and balances for what mods can do, are necessary. But none of that happened. So this attempt at a Reddit clone is just ending up as a bad Reddit clone. Which is probably why Lemmy/Kbin/Mbin will slowly fade away, once people realize that it is just a Reddit clone.
This won't be the final attempt at creating a replacement for Reddit. Eventually, enshittification will destroy Reddit, and something else will replace it. But it probably won't be the Fediverse's attempt at it.
We are now at 48,859 monthly active users vs 51,172 a month ago, decline seems slow but steady. Anything we can do about it?
Link to the graphs: lemmy.fediverse.observer/dailystats