I'd like to suggest adding all the menu commands and preferences into the WowAceUpdater command line parser.
Some of the Ace addons have frequent updates, and some folks have recommended running WowAceUpdater daily before running the game. I already start the game using a simple batch script that does stuff like launch Ventrilo and Thottbot. I could easily start the script with something like:
CmdAceUpdater (http://www.wowace.com/forums/index.php?topic=4778.0) is another one you could try. You can run it from command line with the -u switch, and it will automatically update everything using the settings you specify in the config file. It's also .NET based, just like WAU, so you don't need to worry about installing any other stuff to make it work.