The most obvious thing is that they don't do enough to help you filter the wheat from the chaff. The sheer volume of news that's available is too much for anybody to consume... it is almost literally like trying to drink from a firehose.
So our readers need to do a better job of helping us figure out which stories are relevant/interesting to us, give us ways to skim and summarize without reading the whole article, filter out "dupes", etc.
The problem is that unless that filtering works magically in the background, it just adds interface debris. And it's easy to reach a threshold there, where just scanning for the stuff to filter (hidden amongst the UI elements) and you might as well be better off doing your filtering yourself.
Which right now works best for me. If I use Google Reader directly, it's set up to use the re-reader style, at home I use NetNewsWire with the subscription list hidden. So to browse through it, I can mostly use keyboard shortcuts, so skipping something is easy. Reading is comfortable enough, but if the article is too long, I either open it in a background browser window or send it to Instapaper.
Works well enough for me, although if I had more newspaper-style story listings in there, that just contain the headlines and link to the main story, filtering and adding to the queue might be more difficult.
And alternative would be some kind of social filtering, but that's close enough to HN or Reddit or just listing the links you've got on your twitter inline (c.f. http://news.peepcode.com/)
I use Postrank (formally AideRSS) for this reason - BoingBoing have far too many posts for me to read, so I run their feed through Postrank, and get only the most interesting posts.
So our readers need to do a better job of helping us figure out which stories are relevant/interesting to us, give us ways to skim and summarize without reading the whole article, filter out "dupes", etc.