I don't have a problem with gconf-editor, it's just a tool, rather, it bugs me ( and others ) that the options visible to users are decided by a very narrow view of what people do. If not, the proliferation of options would be huge. That doesn't stop people from wanting to customise, have options, and do things there own way.
One change I would welcome to the way GNOME does things would be to put a visibility flag next to each of the gconf options ( where possible ) to make that customisation available through preferences.
Then we could all satisfy our own use cases without pushing anything on each other.