I do admit, group color wasn't easy to workaround in the bundled skins, but I think I was able to get all the skins looking pretty great with the new tag window, Thunderstorm in particular is pretty great, IMO.
The *only* thing I can see left with the new tag window in regards to skinning is the search bar on the bottom of the new tag window. Look at a couple skins, e.g. Green Eyes, Blue Steel, Black on Black, etc. You can't change the background, nor the font color of the search box there (in those three examples the search box is white with black font color, which doesn't match the rest of the skin elements). Purity, on the other hand, has a black search box with the new tag window and I still haven't figured out how it set that, yet. That's really the last "sore thumb" in terms of skinning the new tag window.
P.S. Since we're on the subject of the skins, does anyone know why the top menus in the Blue Steel skin are spaced so far away from the separator, which is next to the logo? There's like a 20 to 50 pixel space there! Seeing it like this doesn't really make visual sense to me with all that wasted space, IMO.