I agree with both of these suggestions, except that I wouldn't mind seeing replies if they were near the original node (as opposed to just not showing them).

I'm also wondering if it would be possible to be able to mark sections complete. I often start to read the previous evening's posts when I wake up, but only get through one section before I go to work. During my commute, new nodes sometimes get added (or sometimes don't). In the morning it's pretty hard to remember what I've already read ;). Every time I see the home nodes seperate I think about this. It would make a nice configuration option.