Large websites have a very difficult time changing with the times. They trap valuable content deep within them and by their hierarchical nature over time bury the content no matter how well a site is organized.
I think you need to separate the content from the publishing. Social media shows us the first baby steps of how to do this. Content needs to be topical and timely and most of all in the places that people visit most. Government needs to concentrate on creating great content and then distributing it in as many possible ways in the network. Use social media, websites, blogs, mobile applications, groups, comment forums. Wherever the conversation is happening online that is where government needs to publish the content and add to the cultural discourse. Websites are good for storing information but poor at distribution.
You cannot do everything, so build simple websites with great Q&A and search. Spend most of your effort on a getting your content into the network channels and communities who are having the real conversation which aren't heard in washington.