I used Joey for years for Reddit and it has an incredibly useful navigation feature that would allow you to use arrows to jump through every top level comment.
Hey, I'm using 0.49 and to enable this feature, I think you must check the 'show parent comment navigation buttons' box, under the look and feel settings menu.
RIF had the option to collapse all comments by default, so you'd only see the top comments and could expand them if you wanted to go down a thread. I really miss that feature.