How long have you been using Linux and/or Unix systems? Before the Freedesktop.org standard everyone put their config and other user-specific resource stuff in a place of their choosing, typically directly into $HOME or if you were lucky, in a dedicated subdirectory under $HOME (e.g.: ~/.ssh).
To extrapolate your argument a bit: don't you think that /usr/bin is an even worse total mess? Everything ends up being installed there Morale: storing settings files of an entire software family will always remain a mess. This may be why Gnome/GTk use a database (or at least provide a database-like central interface to the settings repository). And you only have to look at the MS Windows registry to know what an incredible mess such a thing can become. The best way to figure out which settings file you're looking for is to look at the file date. And if you want them all in one place you should be able to do that with a simple change (maybe even a configure option) to one of the frameworks. Certain distributions did that so KDE4 stuff was under ~/.kde4 instead of ~/.kde . Doing this upstream would force the decision upon everyone, with all the resulting maintenance costs (each and every application will have to ensure their settings are migrated properly and even then some users may find that they lost their settings). That's not a decision the core devs will make lightly, or so I hope. R.