Customization of the default WPMU blog

I have set up my first users blog on my network.
I have setup plugin commander so that anyone that automatically creates a blog from here will get the plugins that I think they will need to recreate the experience I have tried to set up for new users.

Is there a way that I can configure the plugins and customize the themes that new bloggers will get, keeping all the "setup" for my new users to an absolute minimum?