Perhaps this might be a practical option: We could have a comments board that's like the /dis/ board but it is used for commenting on things posted in other boards. That would be quite awkward to use without a bit of extra support from the site, so it's not quite as easy as just adding an new board. We would want the threads in the comment board to be automatically linked to and from the post they are commenting on. That way people are automatically taken to the correct thread for making comments, and they can always click a link to find the post that is inspiring any comment thread.

In particular, I would put a link to the comments board in the header of each post. If the post already has a comment thread in that board, then the link would take us to that thread and the text of the link would be something like "42 comments". If there is no thread, then the link would take us to the main page of the comments board and automatically setup the new-topic form to comment about the post we came from. In that case the text of the link could be something like "Leave first comment." Naturally for posts in the comment board, the link would take us back to the original post instead of creating a comment upon a comment.

This is probably akin to asking for the moon, but sometimes it feels good to dream big.