Mutter is lean and mean by design, and is for sure way less configurable than Compiz. That's a choice made by the GNOME designers, who place simplicity and maintainability above configurability.

If deep customization is your thing, the best answer is probably "don't use Metacity/Mutter". Compiz is one of your possible alternatives, but there is a bajillion of more customizable X window managers that could do the job for you. Try some of them! From what you say, maybe you could start with Enlightenment and Openbox. And Compiz, yes.

If for some other reason you really want mutter, the grand total of settings you can adjust is 5, managed through the GConf infrastructure (soon migrated to DConf) and declared in a XML schema located at /usr/share/gconf/schemas/mutter.schemas. To edit them, fire gconf-editor and go to /apps/mutter/.

Also, this Fedora Gnome 3 Tips page has a few interesting paths to explore in gconf, and you might find a few interesting not exactly mutter-related but still interesting in gnome-tweak-tool