It's an easy problem to solve, with multiple solutions, but probably much more difficult to implement. Sadly, there's really only a small group of people who engage in any sort of thoughtful discussions as well; which can make QoL things like this a much lower priority.
I personally like how things are currently, but having a way to know which post someone is responding to in a thread where a person makes multiple posts can be difficult.
I'm just praying that the new software isn't similar to diqus or some blog comment sections that mimic it. They can be a fucking nightmare. I hate dealing with the obnoxious loading bullshit, the annoying formatting, expanding comments and all that shit. It tends to end up with everyone piling on the "top comment" just so they can be seen.
No idea what's in store for the future since I only glance when bored, but I hope they don't make the same mistake a lot of places make as they grow bigger by overcomplicating things with useless technology that nobody asked for. It always seems more self-serving than user friendly in those cases.
I say that, but I also know this place is in really good hands, and that they're also members of the community they built. They have just as much love for it as anyone else; if not more. So I tend not to worry since I know that.