why do want to be overdependent on microsoft?
use open standards as html 5. a desktopx skin/theme could be just a website (minus the background). the main program could take care about things like position on screen, z-order and things like a skin options dialog (which the skinner can define in an xml file).
this would make it a lot easier for skinners as plenty of development tools (html editors) and scripts and apis are already around.
this way you could also find developers. or do you know anybody who uses silverlight?