(I'm moving this here from another board)
I assume that changes to colors, fonts, styles, headers, etc., made in the CSS style sheet are overwritten when upgrades are installed.
Why not create a custom stylesheet--editable in admin--that is never overwritten. The <body> tag of the main site can be modified with the "custom" class, like this: <body class="custom">. Then you can override any CSS declarations contained in style.css using the custom class, like this:
body.custom { background: #032c15; }
It just needs to be easier for nondesigners/programmers to edit the color, font and layout of their site. People who don't want to bother will still want to buy templates.