Lastly, as if the other stuff wasnt enough the Nav. pane and favs area on left will not support trans. so unless its hidden (and I assume most people dont hide it, I know I dont.) then it throws another wrench in the fully trans. window idea.
Good points all around.
However, since I...
Rarely use the Start Menu, and never use the search bar
Never use the Preview, Nav, or Details panes (though the latter is skinned at least)
Always use Firefox, which does have the glassed command bar, etc. option with the skin I mentioned
Have plenty of desktop real estate so I never need to full screen an explorer window
...I guess it just worked out that this transparent glass approach worked perfectly for me (re: screenshot above).
But yeah, those issues you mentioned would HAVE to be addressed to make things work for a skin you wanted to take to the maximum number of users.
It's a shame those parts aren't skinnable yet.