Formal Format for Documenting the Game Design Process
Maybe this won't answer your question either, but it might get us closer.


First, a short glance at Jason Bakker's "A GDD Template for the Indie Developer" will stress the need for Breaking down components, keeping it simple, lists are a great tool for knowing what you'll do (as in a To Do or shopping list). Analysis itself being key in the process of game creation.
Second, I would suggest a good look at Stone Librande's suggestion of "One Page Designs". Stressing the need to show the relationship between elements in a more visual way.


Still, I agree with Steven, no tool will ever fit all needs. So:


Lastly, I would add a key component to the process of Game Design: Document Design itself. So we keep this ever-evolving and so that every project has the right document to it. Making the document is the process itself. A living document, changing all along the project.