I've been using Google reader for a very very long time now, and it's besides Gmail one of the most important tools out there for me to stay informed. I don't read newspapers, I don't read blogs directly, I only stop once in Gmail and once in Reader.
The only thing I really consider "missing" from Reader is some way to declare a rule that Reader should never mark a feed as "unread".
Why? Simple: Many online newspapers and sites give out full-text feeds and I subscribe to them to occasionally read some articles.
But, in case of sites like Engadget or Gizmondo, there is no way you can keep up with 30+ posts per day and still do work in between reading. So, my "News" folder in Reader grows pretty fast to 1000+ unread items and I have to go in and mark them all as read every now an then.
I consider those feeds as a constant stream of information, so I don't want Reader to track their read/unread status. If I've got free time I go in there to see what's going on right now, while most of the time I simply ignore those feeds.
What do you think is missing from Google Reader?