##Stock Theme
Please, make a different site design for stock theme. This looks exactly same as Meta Stack Exchange except the lines and meta logo in the header. But that difference is too trivial to notice.
This not only makes the users think that they are on Meta Stack Exchange [Some don't like this and don't feel welcomed here :( ]. but also removes the uniqueness of Meta design. Make some changes to the Stock Theme. I don't think changing the colours of graduated sites with design (e.g. Anime & Manga) sites is very much helpful or makes the users better because they only get the same design as Meta Stack Exchange and common design of Beta sites. Still they don't feel different from Beta site. It looks like putting old wine in the new bottles.
So, please consider changing the themes of Stock Theme and graduated sites without design.