What about a "rabbithole" paradigm for configuration GUIs?

You get very basic settings on the main screen, but there's a button for things a bit more advanced. The screen that follows that button has categories, and each category again has buttons for things slightly more advanced. You go as far down the rabbithole as you feel comfortable. You could have everything be configurable, but it's not a choice between a Fischer Price toy and an Airplane Cockpit.

And, and I think this is a kicker here, you save which buttons you clicked, which screens you edited. So you sortof have your own customized config GUI. It's tailored to each user for whatever they feel comfortable with.