With regards to the Cadillacs, the Hondas, and the Yugos, I have wondered for a long time why we don't allow sites to theme themselves through their own metas. This would involve creating an allowable set of graphical elements (with constraints), and giving site moderators the ability to upload graphics and change color schemes.
Given reasonable constraints, this allows every community to design itself, while still allowing you (the SE devs) to unify your process. You will wind up with beautiful, clearly differentiated designs across the whole ecosystem, all without destroying any of the consistent, unified functionality that you are trying to create.