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Hopefully won't step on anyones toes here but I fully believe a theme should be as basic in structure as possible. Some of the frameworks I have seen that require dozens of files in many directories just get confusing as heck. The intention of simplicity is lost somewhere...
The best themes I have seen have very few files. Makes it much easier to see what is going on and not as easy to make mistakes.
The simplest theme I have seen has a images directory, a theme.html, a style.css and thats it.. The theme its self wasn't necessarily simple but the file structure sure was. Made it easy to see how things worked.
Was able to edit the theme to what I wanted in just a few hours when a theme with many files took me days to change by the time I figured out where things were.
Rodney