Fancy a go on this? I've re-written the texture baker - as I didn't like the way it went about things.
1.24 patch by Christoph Kubisch - added 'save frames' option to bake animations into a sequence of images
This new on uses linked lists of bake channels - so you can share channels between objects and set multiple objects up at once. It also frees up the ability to render different channels on the same object at different res's.
It won't set up auto unwrap options on objects because I don't belive you can leave a job as important as UV mapping up to a totally automated process. It just bakes.
You also don't need to go back and forth to the scene to add new object to bake. All baking properties are in the dialog and you can do all your set up from there.
The channels list always shows channels that are shared between the object selected in the list on the left. It should be pretty easy to work it.