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Currently many distros devel creating tools to help user in one's system, like Mint, etc. Some are working on own Desktop Environment. Also many installers are wrote in GTK+ or Qt. Also many small programs could better suits/integrate with Desktop Environment.

Solution? Write Administrative Toolkit, a wrapper library above GTK+ and Qt and possible others. It will load backend (Qt/GTK+) on load by currently ran Window Manager or by user settings. It will allow only to do simple thinks, but also provides extensions, so:
1. GNOME could support headerbar extension (if not present, application shouldn't use it)
2. KDE could also support some extensions
3. Each supported backend could provided the same list of extensions or different (Look at OpenGL API)
4. You could construct API to allow backend to choose to turn on extension (for example - if you create api for dialog with choice between yes/no, GNOME could but buttons on the headerbars, while KDE may select other way) - Administrative Toolkit should been constructed to not allow to developers do too much, because maybe we need to change something in future (Desktop Environment paradigm) - it should been created to make it evolve in mind, not giving power to application developers.

Why this?
1. Company A could wrote installer of some game - it will looks nice in each DE supported by this toolkit
2. Mint developers wrote configuration tool for one's system, which didn't use distro-specific config file - why don't use it in other systems?
3. My small program looks nice and integrate well in both KDE and GNOME world

Most frameworks provides similar widgets set and similar options. I don't wrote we need one framework for every app, but to allow some applications to integrate well in both world. Also some distributions could remove GTK+/Qt from standard installation (in far future of course).

I don't know much about libYUI or wxWidgets, but you can use another project (one of this?) as a base.

Two thoughts come to my mind reading this...

1. The issue is not that it hasn't been tried, this has been tried time and time again.
The reasons speak against this: 1. system configuration is more complex than you would expect, even if not considering different desktops. The current tools are more or less advanced, but non of them even succeeds in really offering a fully working configuration tool. They all only handle the basic things, for all the rest you need to dive into the command line anyway. So in a way you can call the command line the universal configuration tool you ask for

2. the first reason you cite is not a reason at all. A company should _never_ provide their own "installer" to whatever software component they offer, be it a game or something important. Linux systems come with a well working, secure and proven software management system, that is how software is installed. Enabling company or product specific installer options modifying the system are a mile wide security thread, it will lead to chaotic situations like we can see in the MS-Windows world. No thanks.
Companies should learn how to pack their software so that it conforms with the available management tools. Many companies refuse to or are unable to, but that should not lead to waekening of security and comfort in a Linux system.