I would argue that the current form of Lemmy (and kbin, and lotide) is a lot like a forum, to the point that there's a phpbb front-end.
I think the key to long-term discussions is going to be having small enough communities that you can recognize the other people you're talking with.
Once you recognize the person you're talking with, then the conversation naturally becomes a continuation of the last one.
My soapbox instance is a good example. There's a number of people that I routinely have discussions with, and because I recognize those people and I know who they are, and I know where they're coming from, we don't need to rehash earlier forms of the discussion. Instead, we can keep the conversation going even though the Twitter style conversation thread would suggest that you can't do that.
One of the things that I think will help in the long term is having profile pictures. Somebody who's having a conversation with me may not remember my specific name, but the icon next to my message is going to be the same and so they will remember the last time that they had a conversation with me.
I think that that sort of long-term conversation also might help with some mutual tolerance. You see someone, and you know their views and so you end up having a conversation with the person rather than with the class of people that they represent.
I think that's one of the biggest problems in political discourse online today, is that instead of people having conversations, people have conversations with classes of people as represented by one other person. In that way, there can't be any nuance because not agreeing with the class that you represent is itself a sort of own, instead of common ground two individuals can agree with.