I am wondering what do you do about the fact that the comments etc. are not available through RSS feeds. Aren't the comments equally important part of the news itself?
Starting at the top of HN and reading down comment thread by comment thread is a recipe for hypertension. Instead, pick a couple commenters you like (my list is on my profile) and follow them. I have a list of bookmarks for each of the users in my profile.<p>An advantage to this approach is that those commenters also screen stories for you. You can glance at the front page and click only the very most interesting stories, then go read all of 'potatolicious's comments to get a glimpse of what he found interesting without having to click from thread to thread.
I actually mostly read the stories directly in my email client, and only then I may now and then check the commenst on specific stories. Like tptacek said, reading all comments is a good recipe for hypertension and since HN has become more or less very prone to flamewars et all.