I believe that the lack of built-in useable statistics is WordPress' biggest weakness.
Every WordPress author needs to have complete, accurate, and timely access to their blog statistics. Many of the add-on stats plugins make modifications to the DB, and this puts the entire installation at risk.
I have personally had a fairly well-know stats package fail, leaving my site crippled until I was able to repair the damage and bring things back online (without the stats plugin).
We need the developers to think through all of the different statistics that people will want and at least build the data collection function into the core of the software. Then you can allow plugin authors to simply slice and dice the data that is already being gathered.