I'm a little torn on this. If skins evolve within Wikipedia (and foundation projects) but not on mediawiki core I won't feel like we're putting out a good product.
I know what you mean, but what I'm calling for is really minimal: identify a UI feature which that could be usable and attractive in two variants (like two different shades of grey for the background of the Vector sidebar), and choose one for the default for core, and the other for Wikipedia. You can include the Wikipedia-specific style in core; just gate it with a configuration variable. Most third-party MediaWiki instances aren't styled the way they're styled because their administrators wanted to mimic Wikipedia, but rather because they find the defaults sensible and useable and didn't want to fuss with things. We should continue to provide defaults that are sensible and usable, but we should pick one -- just one! -- and make it sensible, usable, and slightly different.