I think this can be done by modifying the theme of Emulation Station. As a result, this question is more for Emulation Station, than for RetroPie.
You can find the default Simple theme on your Raspberry Pi in this directory: etc\emulationstation\themes\simple
There you will find information specific to each console. For the main menu, and system-wide changes, look at the “simple.xml” file, and the “art” folder in the above directory. I believe you can change the color of the background by creating an 8×8 square of color (like “bright.png”, “dark.png”, etc), putting it in the “art” folder, and then modifying the “simple.xml” file to point at the new color file.
Anything beyond what you see in that directory cannot be modified. You can do quite a bit with just the theming system, but anything beyond cosmetic changes is impossible for now.