I think I understand the system settings.. it is in fact system settings, settings that change how your system behaves. It isn't exactly a place for apps to put themselves.
That said, we don't really have a proper forum to educate developers on how to write applications the "GNOME 3" way. I realize we direct people to #gnome-design, but that's not really enough.
To look at the big picture a bit, if we were to construct a life cycle of a GNOME application on how a developer goes about writing something in GNOME 3, we aren't going to get very far. For instance,
developer.gnome.org is not anywhere on the gnome 3 site so an app developer at the moment really has to work at getting the information they need to get going. That's something some of us will need to work on...
A simple construction of:
in GNOME 3 - where do I store configurations?
In GNOME 3, you must store configurations in gsettings and stored used in
edit->preferences menu items. If you're app is a part of core GNOME 3,
you may put your settings in system preferences
Would help I think in giving application developers an idea where to do put their settings and avoid the abuse of system settings. You can illustrate using "good" applications that do it properly like say Rhythmbox and Totem.
In the end, nobody can stop people from abusing the system settings if they wanted to. The source is out there and distros can just as easy revert whatever we do.
sri