Thanks for your reply and let me say first of all great job on NodeBB!
I happen to be a big fan of the branching/threaded/nested/hierarchical (or whatever you want to call it) comment structure, and I think the format, when properly implemented, is the future of discussion formats. I am particularly enamored with the functionality of a typical reddit discussion with RES (reddit enhancement suite) installed. One has the ability to hide or show all child comments, so if there is a sub-thread that a reader chooses to follow or dismiss, that thread is easily expandable/collapsible. As far as getting lost within a thread, the marker lines that connect comments and reply text boxes are fairly effective in determining which comment is being replied to. I think what would make it even easier would be to add a tiny bit of JQuery so that by clicking on the line would allow a reader to jump to the original comment.
I also feel that the ability to vote on comments (the karma system) can be a huge benefit for communities, especially smaller to medium-sized ones that haven't the luxury of several full-time volunteer moderators. Aside from such a forum having a necessary default anti-spam system in place, the comment karma system allows such a community to effectively become self-moderated, eliminating the need for bots/volunteers (for the most part).
Thanks for hearing me out. I'll keep a close eye on developments with the NodeBB project and will recommend it to colleagues who are looking for clean, modern, linear discussion formats.