For example I run a job board, the metrics I care about are how often candidates come back to look for new jobs, how many candidates look at each job, how many apply to each job, how this is related to the skill sets for that job, etc.
Technically I can (and do) get this data out of google analytics using a combination of regexes, custom variable and custom segments and a little voodoo. But it's essentially a hack.
Google Analytics feels like I'm using Atari Basic where page urls are line numbers, when in actuality I want to be writing in Python and be talking about business objects.
I want a web analytic system where I can tell it about my business objects. If a user goes to a job page I want to be able to stick some javascript in my page which goes analytics(object="job", action="view", id="232") and then lets me do sophisticated analysis on user behaviour.
I don't want web analytics, I want business intelligence for the web.
It could even hook directly into your database allowing you to merge your business object data with your usage data.
I've used both, but just rolled my own system.