Personality cults were a regular theme. Honestly just one individual with no other goals in life could wreak havoc by constantly weaving between the rules, launching sock puppets to do some virtual Munchausen-by-proxy performance, painting admin as the bad guys, staging crises that didn't really exist to get more followers (in the social sense, there was not really a "follow" option in the platforms at the time). These topic-based forums were often in direct competition, and on more than one occasion it was revealed (usually by infiltrating via long-term social engineering so you could get to see the IP addresses of the members) that these users were from competitors trying to stir trouble and siphon off members.
Diversity and cliquishness was an issue. Generally a community would kick off around some exciting new theme, or just a general shared interest and grow organically from there. This was great but the longer the same group hangs together, the more insular the atmosphere and inside references became. It's just what groups of people do in physical groups when they hang together a lot - they grow bonds with each other, their shared experiences strengthen these bonds, and newcomers see this and can see that it will take a lot of effort and patience to reach the same level of acceptance, and the older and more insular a community becomes, the less people are attracted to it. Then eventually the older members see there's nothing new to learn here and drift off. So the lifecycle of topic-based message boards followed a standard inception/growth/stagnation/diaspora pattern.
Generalised social media puts everyone on an even platform - albeit a pretty shitty one - everyone sucks equally by default. You're correct in that the centralisation has a ton of other side effects and I don't disagree that many of these aren't what people want (if they're aware of it). Just that as I said it wasn't all roses and we can't just "go back". There were tons of reasons why the topic-oriented message boards faded away and it wasn't just laziness or convenience. It is human nature to desire connection and a sense of place, balanced with a need for novelty and invigoration of ideas. Generalised social media provides that routinely and formulaically, they basically hacked our brains.
Also on practicality of your suggestion, we can't force people to go back. You can't put a gun to people's heads and force them to only use single issue forums. I get the nostalgia because I was a part of it and it was great for a time, but it did also have a ton of downsides.
I think we need to move forward not go back. Federated social networks are one attempt at this. It's a lot to take on board as we have to learn new things like managing our identity / signatures and learning differences between providers, but efforts are underway to try and shift us away from the big old attention silos people have been trained to use these days.