Sorry to revive this thread, but I have something to add.
I, myself, are pretty happy with the flat discussion model for my own communities. However, when recommending Discourse to others the topic of threaded discussion usually comes to light.
A person I know already has good experience with the threaded discussion model (1 level of nesting only). The idea of the community they currently have is that the first post is somewhat of a prompt or a real-life account, the first-level replies have their own titles and start actual discussions inspired by the prompt, and the second-level replies are like regular messages in a discussion. This tends to work really well for what they want to do.
I would like to recommend Discourse to them so they can benefit from the great UX, post editor, slow mode, drafts, and great administration features. I would even offer to personally set up the forum for them, but it’s hard to do when this person has really good and proven experience with this discussion model and doesn’t want to change it. Currently they’re running a blog software modified to work as a forum, but the solution is starting to show its age in terms of features and stability, and was never a good idea to begin with in terms of maintenance.
All of that said to explain my use case, I think it would be a good (optional) feature to allow 1 level of nesting in thread comments. I understand there is no UX for this, so it would be complicated to do. This is just a long-term suggestion, but I think this would be really useful for certain types of discussions and communities.