Starting with what i think will be the best feature, Color Customization:
In the themes page (if this gets added), users have common colors used in the website, with the place they are used listed on the side. When clicked on, they present a color picker, that updates dynamically as the user chooses an color.

Fonts
In a separate tab on the themes page, the user can select a default font to be used in the website, including Minecraft's own font (Mojangles). The choice does not affect custom fonts in user-generated content.

Backgrounds
In another tab, the user can pick pre-made backgrounds for the dirt/blackstone bricks BG, the sky and the border of the background.

Optional features:
- Changing the PMC logo
- Let users set their page to always display a theme, similar to jams
- Let users set their page to always display the default theme
- Sharing themes with the community

I bet many users would love this addition, even more when setting a custom theme to their own page :)

EDIT: Now that i got more time, here are more suggestions:
Theme page will be accesible in the My Account page, url maybe planetminecraft.com/themes?
Tab system is like settings page

Maybe for some blank backgrounds we can select patters, think Firefox Color