This revisits an idea posted here a week or so back which never got intelligent discussion because of personality/style issues.
The concept was to create an option, within WordPress itself, within a specific theme, or as a separate plug-in, which would allow complete design freedom in building a site header. Specifically, this would be a space/area within the framework of the page where somebody could insert HTML, Java, etc., which would look and behave as if it were standing completely on its own. Personally, I would use this space to do what I (still) refer to as "image mapping," or one form of it. That is, I would start with an image equal to the size of the available space described above, and I would use it in a number of different ways by slicing it into pieces and then selectively substituting other design elements for some of those pieces. In the past, I have used this approach both with and without building a container table. In essence, this would be a "neutral" space in WordPress that would act as a completely blank slate. No combination of widgets or whatever accomplishes the same thing.
I'm told that this could be a tricky piece of coding, and I'm not a programmer, so this is a suggestion/invitation/request to somebody who is. It's hard to imagine that a lot of people wouldn't find this kind of capability extremely useful. The same concept could be carried over to the sidebar and footer areas, although those are already more flexible than headers seem to be. Even so, as an approach to accommodating the widest possible range of design options, this still exceeds anything that is now available.