One major flaw with Google Analytics is its last click attribution which simply distorts your view of where traffic is coming from. If visitor first came via a Tweet, reads about your product and the next day he searches or types in your web address, GA would attribute the last traffic source as the real source of this visitor. You would never realize that it was tweet that brought him to the website.<p>Seldom any visitor converts on first visit and so it becomes extremely hard to calculate true conversion rate for different mediums in GA. How would you know which medium is most effective?
What are really good resources on using Google Analytics? I don't check more than my pageviews, referrers and popular search terms, but I know that barely scratches the surface of what it can do.
You should also have a look at my server-side Google Analytics client <a href="http://code.google.com/p/php-ga" rel="nofollow">http://code.google.com/p/php-ga</a> which opens the door for many many advanced usages.