I do agree, threaded chat seems challenging. I feel like I most liked Mattermost's setup where everything that was a reply to can be opened up side by side with the existing chat. Nothing is hidden by being in a separate thread, its obvious when something is a reply to, you can also just jump to the last reply to in order to get more context, etc. Obviously, tradeoffs with every style. Speech is messy no matter the medium it seems and everyone has their own yum.