They'd need to port all their Gtk/Qt apps to it or abandon these.
Both Gtk+ and Qt already run on non-X11 platforms like Win32. Canonical would simply need to add a SurfaceFlinger backend to the frameworks, and then the apps would just work.
The number of modern Linux apps that use X11 directly is small. Anything that makes substantial use of raw X11 is not going to feel "native" anyway by modern standards, so I doubt that Canonical would feel bad about abandoning compatibility there.