Skin system rewrite currently supports old, SkinTemplate/QuickTemplate-based skins. For example, Vector uses SkinTemplate and QuickTemplate and it works well -- but as noted earlier, it won't support some of the new features (SkinAfterSidebar hook and whatever else we may add in the future) until it's rewritten. So no worries, you should have plenty of time to rewrite your skins. :-)
Thanks and regards, -- Jack Phoenix MediaWiki developer