What i would like to see is what you already mentioned. We are working on a View Layer for a Windows Application and want to throw away our old "windows xp" look and set a new layer on top of the application with the web.
Some things are really a pain to change with pure css like checkboxes, radiobuttons and scrollbars.
I know you should normally NOT change the look of the scrollbars, but we have a really dark and minimalistic design, and the bright 3D scrollbars of some browsers just don't match.