I still have a link to comments for each story in Google Reader (although I don't get the number of comments). What I gain with Reader is the ability to mark all as read and therefore the ability to see what's new since the last time I checked.
"I still have a link to comments for each story in Google Reader (although I don't get the number of comments)"
If you browse comments a lot you end up spending almost all your time outside the reader anyway, so it doesn't seem to help that much. I can see how you want to avoid the frontpage if you check HN often - it just shows you the same stories all the time.
I've thought a lot about this, and RSS doesn't really fit social news, especially comments. So far the best UI I've been able to come up with is hackerstream like I said elsewhere in this thread.
If it seems like the comments might be interesting I just click the 'comments' link.