Well I still prefer if developers try to build a GUI that can do both. Sure, it's more work, sure it is harder - but if you succeed you got really a superior product. Some applications manage to do this - a great example is gwenview 4.x, which is 1000 times simpler than its 3.x version but has actually MORE features. It's possible ;-)
Something like GConf is just an abomination, imho. KDE has something like that kconfigeditor I believe - blegh. I must say I like recent ideas to build in search in configuration interfaces, let them be build dynamically etc - that might be very helpful.
Finally, why install a separate app or tool if you could have an advanced button in a normal gui hiding the complexity but having it available for those who need it?