I finally switched over to Google Reader from Bloglines after it failed me for 2 days in October. I have a few gripes of my own and wonder if Google will ever address them. For example, I don't understand why there's an incredibly annoying amount of whitespace on the right side of RSS feeds -- Google's decision to wrap text in the way that it does is, erm, annoying.
Another problem I don't like is that Google Reader can't tell me exactly how many feed items I am behind on if there are more than 1000 unread items. I have to say that I liked Bloglines telling me when I had 4342 unread items. 1000+ could mean 10000. Seriously.
A third problem I have is that I'd like to change the text of Google Reader instead of using the old school Arial. In the meantime, I'm hacking userChrome.css in Firefox, but I really shouldn't have to.
Other users are observing other issues with Google Reader, and believe it or not, I've experienced them also (but then again, if you're a Google Reader user, you probably have too). Sometimes, Google Reader says that a specific feed has one unread item. However, you may then enter that feed and find out that there are no unread items at all. It's misleading to say the least. Google Reader Guide says that "we've noticed that unread counts can get thrown off as result of tagging items from feeds you aren't actually subscribed to or by subscribing to another user's shared items feeds multiple times." Neither of these impact me, but I do see this happen ever so often. My solution is to "mark as read" and then usually it goes away. The key word here is "usually."
In any event, Google Reader Guide seems to be aware of this issue as it's still impacting a number of individuals.
Forum discussion continues at Google Groups.