Ditch X11 and start over. This should be something that is assumed to only run local and will have direct access to hardware. while compositing window managers take a step in this direction, jump in all the way.
While it is impressive that you can direct an application to use a remote display, even an underpowered PC can host a native GUI that runs locally and is accessed remotely via VNC or RDP.
Combine it with a standard UI widget toolkit that is constant and don't waver. Do not allow co-mingling of various widget technologies, the current state of X11 allows such a diverse assortment of UI toolkits (KDE / GTK / etc.) that you are destined to get apps that look and behave differently.
Users don't need to theme their desktop, it is usually more important to them that it looks and behaves the same on every computer it gets installed to. The last thing a user wants is to sit down in front of an app and find that it looks completely different.
Finally, build a killer visual IDE that is as easy to use as VB.NET and use this to construct all of the apps your new desktop. That should just about do it... It wouldn't hurt to OEM bundle it with a few large PC vendors.