I merged all three files together (layout, font, color) for my fixed-width theme. I went one step further (as did Joseph with Orangechoc) and eliminated using the standard theme. I hacked Moodle quite a bit in this theme and didn't want massive cascades or load times. For example, I didn't want to load my tab img files over the standard tab img files.
In reality, however, I'm not sure my efforts paid off. I still have a big, fat, complicated theme!
Basically, here's what you need to ask yourself:
- Will you be the person doing all editing and upgrading in the future? I ask because, if not, you may want to stick with Urs's suggestion and not stray from the Moodle css format. The difference between your theme and the standard theme could confuse a third party (as in the case with trying to modify Joseph's Orangechoc).
- How modified will your theme be? If the answer is 'not that modified,' then I wouldn't mess with the structure for practical reasons - like time.
- Do you plan to share your theme with the community? If so, you may want to keep the structure that we're all familiar with.