I don't have a good idea of what's possible, technically and time-wise, but here goes: what I propose is an in-game resource manager that could also double as a theme editor.
An embarrassing mock-up:

You could browse through lists of all the resources installed; necks, backgrounds, meshes, etc., which would also be immediately viewable in the preview section of the window. When you go to select glows/hitflames the notes would freeze in the 'hit' position. Other settings such as size and flame/note color could also be edited. Options such as basic colors, sounds, mods to be loaded along with the theme, and title graphics could be set in another menu.
When all settings are set, an .ini file could be saved, and the theme would then be easily selectable from a separate menu located elsewhere in the game.
So, what do you think? An impossible fairytale? A useless feature not fit for FOF? An amazing idea that must be started upon immediately? :p
If you have questions about the idea, I'll try to answer them.