While I appreciate minimalism I think the comments page is lacking. Let me preface my complaint with the fact that HN is probably the only site I visit frequently, due to the quality of posts and commenters.
My biggest complaint is this: I enjoy reading the comments of submissions, oftentimes more than the submissions themselves. It's really frustrating to read a post with many comments in the morning (lets say, 40), then come back at lunch and browse the same comments when there are more (say, 45 - I often leave interesting posts open in tabs to look at later). Obviously these numbers are arbitrary - think of 10 new comments on a page with 100 or more! Without a clear indication of what is new after a page refresh, I have to re-read every comment and compare post times (or effectively recall reading that comment previously) in order to see what's new. Compounding that is that the post order can change.
Unfortunately, I'm not aware of anything that can be done to fix this. To me, that is a usability defect. Enough for me to stop visiting? No!
For logged-in users, Scoop (Kuro5hin's software) keeps track of when you last visited a comments thread, and displays a [new] next to all comments posted since that timestamp.
What's more, comments are really difficult to read on a mobile phone, which is surprising, given that they are basically just plain text which should have the virtue of being easily reworkable.
That said, HN rocks, so I can't complain too much.
I'm not talking about ugly or beautiful, I'm talking about very specific usability problems. For example, it's very hard to tell when someone replies to you, which means I would just drop out of conversations if they didn't appear on my "threads" page. (Although there is a solution nowadays, notifo). HN also has problem with the voting, like being unable to change votes, etc.
That said, HN still rocks. Does the incredibly limited UI have anything to do with it? I don't know. But I wouldn't mess around with HN too much: why mess with something that works?