A possible way to do this (Score 1)

A great idea! Here's one way it might be done:

1. Each application continues using it's own config stuff, ie. dotfiles, and settings can be changed as they are now, or with the common system. The common system ends up changing the dotfile too.
2. The common config system is an interface to the dotfiles. Application writers or other volunteers keep up an e.g. XML file that defines what the config options are. This file would define how the dotfile is formatted, where it's stored (system wide and personal) and have names, value types and descriptions of all options. Actually a separate file with descriptions in different languages would be better.
3. There would be various front ends to the config app, as described in the article, and it'd display the info from the dotfile in the format specified by the XML file.
4. root would get the possibility of changing system wide or personal settings.
5. When an application is installed, this XML-file would be moved to eg. ~/.config/appname.xml, and the front ends would know to look for the stuff there.
6. The system should be smart enough to display system wide settings and default values as current settings if the user hasn't changed the config yet.

Just my € 2 cents worth...