For threads that are getting a huge number of replies, it might be better to have them as multiple separate threads.

If they are consolidated they become paginated, and pagination does work well for rapidly growing nested comments.

What I see happen is that I get to the end of the first page of comments, then go to the next page...and actually see many of the same top level comments that I had just read. While I was reading them the first time, the new comments and replies coming in sufficiently shuffled the order around to make much of which I just finished now be second page.

I think that to make pagination work well, time must be taken into account.

Simplest would be when a thread is rapidly growing to change the ordering to be strictly oldest comment first.