The problem with "by top score" is it would itself influence the scoring, even if only some people used it. The oldest comments would stay at the top of such a list, because they get seen more and thus have more opportunities for upvotes, creating a self-sustaining cycle. You always need a time counterweight.
That would be nice. And also a way to wrap all comments that are replies to first-level comments so that we can see all these and only reaf discussions on projects that interest us.
Sorry, it may not be the right word. I mean the effect that clicking on the little "[-]" does. A way to automatically clic this for all second-level comments, so that only first-level comments that directly answer the "Ask HN" appear.
If you find a place for comments sorting options (what my parent comment initially suggested), it could go there too (it's also related to comments display settings).
Maybe a line between the "add comment" button and the first displayed comment?