> ...it would be great if replies at a certain depth were collapsed automatically...
I agree: I love that feature. However, Reddit then has the problem that you often find a really stupid comment rebutted by the most exciting and interesting comment on the entire thread; in such a situation, the stupid comment gets downvoted and manages to auto-collapse away the juicy gold hiding below. Slashdot handled this better: they auto-collapse threads, but if an auto-collapsed thread contains a highly-ranked comment, it "bubbles out"... as in, you can still see it, even though its parent has been collapsed... I'm not certain how to best describe it, but it is amazingly useful.
> I also wish there was some way to encourage concision in comments. ... The article itself is only 1541 words (and I didn't read the whole of that either).
This community seems to encourage well-thought-out replies; I could technically have posted a "blog response", but I find it more interesting to end up in conversations in the comments of the articles where I think of things to write. (I may actually soon start a more real blog, but I've always seen that as an awkward way to do back/forths.) Personally, I find the longer comments to be the ones that are more valuable, and would rather short comments be discouraged ;P.
(Another solution to this, btw, is to just have comments get collapsed to something that then has a "Read More" that inline-expands to the full comment; this is how Facebook solves this, as otherwise it would become a problem that your Timeline or Newsfeed was dominated by a couple very long posts instead of being an overview of the material available. As someone who actually does read and value long comments, however, I have mixed feelings about this. I mean, if you didn't read the whole of the article, it becomes difficult to really comment on it effectively: it doesn't take that long.)