You like getting news from aggregators like HN/digg/reddit? Great! Do you think that news is well-presented when you find it (via the above aggregators)? That's a completely separate question.
In both scenarios (reading HN/reddit or reading the NYT/Chicago Tribune), you're consuming content from some sort of layout. I think it's fair to compare those two to each other.
News websites also need to maintain visual continuity between the navigation and the articles themselves, while aggregators only need to design navigation.
And a news site can still have a simple headline page AND consistent when you click through to the articles.
Also, I'm not saying there's no room to add emphasis and prominence to some articles, but I am saying that the way they do it now makes no sense to me, and I'm a designer by trade.
News sites are written consistently. All news stories follow the same format, with the first paragraphs summarising the story. The news site knows if a picture in the story is relevant.
Reddit & HN actually tell us nothing about the best format for news because they quite literally can't serve their links up in a format like this. Each source is too different.
Though I also think it's too busy. But I do not agree at all that HN or Reddit can tell us anything about news sites.