Something new that we hope to have in core is a theme manager package. I've already cleaned up and set up a primitive start on HEAD, that for instance removes the hard-wired values for admin sub tabs put in by Lars out into parameters so you can actually modify them, plus a somewhat clean way to declare and change theme elements like css files and master templates.
Emmanuelle Raffenne is working on a more thorough proposal to break it out into a theme manager practice, and also include things I ignored like paths to directories including icons, named CSS for including high contrast or other custom versions, etc.
The difficulty here will lie to a large extent in not making it break existing customized sites, or at least making upgrading simple.
