Yeah, AS 3.0+ seems to do that to me as well.
But there really shouldn't be a difference between a new Android Resource Directory and just a new (regular) Directory if you don't actually use any qualifiers. It's still just a directory with a different name depending on the qualifier(s). So, you can safely choose new Directory and move along.
And for the sake of it, you can choose new Android Resource Directory with some random qualifier which will just add the qualifier to the directory name, and after it's created, refactor it by deleting the qualifier part from the directory name and you'll end up with a directory named "layout" which is an "Android Resource Directory".
Just do the refactoring with the Project view selected in the Project pane, not the Android view.