Those are fair points. I think it depends on if the majority of replies to a topic tend to be comments on the main topic, or if there are a significant amount that are direct replies to other replies (just my opinion, but I’m not a fan of the extra step of quoting text elsewhere on the page, but it’s not the end of the world to me).
Let me give that one some thought to see if there’s a happy middle ground. Possibly a link/button at the top that flattens and re-sorts the comments so that both methods remain available? Will think on that.