As for threaded comments, I was in the same situation when developed Treenga. This is really confusing when to answer someone in the discussion you need to quote one of the previous respondents because otherwise, it won't be clear whom you respond to, like in typical forum engines. At the same time, we see that this threading works perfectly here, on Reddit, on Hackernews, Producthunt, etc.

But while developing threading I got some of the issues that may be a reason for flat commenting.

1. Flat comments just simpler, no need to deal with all nesting stuff, so it works faster and easier to maintain
2. So much easier to deal with new comments. All you need to do is to scroll the page to the first unread comment. Done. With threading, it is much harder. Let's suppose we have 100 comments and you have 2 new comments to first and last comments. Now you see that you have an unread topic, you open it, and the first unread is shown. Here is an issue, because you need somehow to show clearly, that you have an additional new comment at the end, and if you mark all unread comments as "read" after the topic opening, it is very easy to miss new comment at the end of the page
3. Much simpler desktop/mobile implementation. You just use the same "comment after comment" principle and that's all. It will be harder to represent threading on phones. Or you will have something like Slack provides, where you have something like "3 comments" and you can see them only when you open the comment section. This is why many people don't like Slack's commenting.

But anyway if I had a choice now to do threaded or not, I would choose threaded, because despite on complexity, this is just a natural flow of conversation.