Since now the skins seats under the new "App_Templates" folder, why in the world the "skins" folder was kept? Seems to me that it is completely unuseful unless to confuse the developers.
I was used to the old folders structure, and I longed a little while to figure out why the changes in the template.ascx wasn't reflecting on my website before to find the new "App_Templates" folder and the "template.master" file.
Also, I don't remember to see this change documented anywhere.