Kill $wgSkinExtensionFunctions. Way back in r4934 when it was introduced, it was near the beginning of Setup.php, and $wgExtensionFunctions was near the end. Thus, they served two different purposes for doing extension setup. Refactoring over time has brought these processes side-by-side and thus the unused (and less-featured) one is getting the axe.
-1 more awful global \o/