“sudo notepad /boot/home/config/foobar”
I don’t know where you got the impression that one would need to open a text file in one’s home folder with sudo from the command line, but this is wrong in so many ways. You can just double click it from the file manager on Linux distributions as well as on Haiku. Not a single visit to CLI land is necessary for that.
Also the config folder does not only contain settings, but a whole bunch of other stuff. You should take a look at it when you get a chance. Your suggested solution has several problems too. It clutters user-owned files in the filesystem, makes owner ship management and backups harder and doesn’t add any real benefit other than hiding a folder.
You do have a point, though, and although I don’t agree with your reasons, I think Haiku should have a unified and endorsed way for programmers to save application preferences. That’s something almost every program needs and yet on many platforms there is no simple API for that. Mac OS X has NSUserDefaults [1] for it and Android uses SharedPreferences [2]. Systems like GSettings in the Gnome world and the Windows registry got the premises wrong and are thus not nearly as comfortable to use.
However, Haiku is “almost there” and doesn’t need something like libelektra or a “registry”. There is BMessage, which can be flattened (stored) to and unflattened (restored) from files. This is sufficient for almost any kind of preferences.
What I’d like to see on top of that would be roughly something like a be_app->GetPreferences(), which would return a BMessage and be_app->StorePreferences(BMessage). This way the OS could decide where and how to store the actual physical data. Which would mean 2 things: a) application programmers don’t need to think about tedious stuff like storing preferences and can concentrate on more important things and b) it allows for something like OS X’s defaults system [3].
The important thing here is, that the application does not decide the where and how, but the OS does, e. g. by using the app signature.
Once applications would use such a system, moving the settings without breaking app compatibility would be an easy thing to do. If one would really want to do that.
Also, calling Linux an “insuccess story” comes across slightly disrespectful, considering it runs on a majority of the world’s smartphones and an increasingly large number of desktop computers. Valve is planning a game console running Linux and it’s in more embedded electronics than you’d think.
[1] http://developer.apple.com/library/mac/#documentation/Cocoa/Reference/Foundation/Classes/NSUserDefaults_Class/Reference/Reference.html
[2] http://developer.android.com/reference/android/content/SharedPreferences.html
[3] https://developer.apple.com/library/mac/#documentation/Darwin/Reference/ManPages/man1/defaults.1.html