WPF just got some love a few minutes ago - they've got plans for a new release of it by the sound of things.
Result: we now have to ship a .reg file to our clients before we can launch our shit via ClickOnce. That's only 2000 people we now have to hand hold through this.....
There is no straightforward migration path from vdproj to WiX, either. It's a case of re-writing all of your deployment code (which has already been tested/tweaked/hacked on for years) for no upfront benefit.
http://www.add-in-express.com/vdproj-wix-converter/index.php