While I like Reddit, the problems you mentioned become apparent when you look at /r/depthhub, /r/bestof and /r/defaultgems. (On a sidenote, is there a way to find highly upvoted comments on HackerNews?)
While they work as well for finding comments from subreddits you are not subscribed to, they help with exactly the problem you mentioned:
>If you are a slave to the parent-child reply hierarchy, you could have the most brilliant upvoted post in the world, trapped way down deep in branch 5 of the tree where nobody can see it.
I think the threaded system is best if you are deeply invested in a discussion. It helps better than any other system I know of understanding what’s about what. Especially when the discussion is a huge one you can easily find the parts of it that are of interest to you.
When I read a thread in a bigger board they often get to topics I have no interest in, how would I wish I could just press a + sign and collapse that part of the discussion. And threads with thousands of answers like Reddit has quite often? I don’t even try to read those, without threading that’s just a giant wall of noise for me.
SE’s 2-tier system (Q||A)&&C is great (perfect?) for what the site does but for proper discussions? I’d take threading every day.