Hi Paul,
The product configuration in Catalook still makes me whence on some projects I face. However, it's mostly due to how bloated it is that makes it most confusing. I still have to catch myself from time to time and remember this cart was made as a catch-all for damn near every business type. Enough said.
On to your particular issues. Can you please give me a specific product setup as your "ideal" solution. (i.e. if it were the way you wanted it, it would look and act like...)
This will help me out in learning exactly what you are out to accomplish and I should be able to configure a solution to meet your needs without too much of a headache.
There are SQL scripts that can be run later to allocate different configurations and attributes to the products in a logical manner. We just need to set the baseline.