Hi Tom,
a few suggestions wich maybe would improve and extend the customization for each element.
Page-Header / Site Header:
Ability to set a custom Navigation. Actualy you can position the Navigation to another location. Would be cool to set a complete different navigation.
Layout / Sidebar:
Ability to set a custom Sidebar size. So if you define a custom layout for a specific post type – you can set the sidebar size here directly.
With the new display rules this would be a big improvement in my opinion. So it is very easy to customize the Website more and more.
I know you have a lot of ideas and a lot to do. These are just my ideas while testing the Beta 1.7.