You cannot use Windows Store Apps specific plugins if you use Windows Store Apps API like this http://msdn.microsoft.com/en-us/library/windows/apps/br211377.aspx in Unity Editor, so we changed a bit how Unity Editor handles them. So basically you make two versions of plugins:
Both of them must share the same name. For example, you should place Editor compatible plugin in Assets\Plugins\MyPlugin.dll, and Windows Store Apps specific plugin in Assets\Plugins\Metro\MyPlugin.dll. When you’re working in Editor Assets\Plugins\MyPlugin.dll, and when you’re building to Windows Store Apps Assets\Plugins\Metro\MyPlugin.dll will copied over.
You can also select which plugins should not be processed. Simply specify plugin file name in Player Settings -> Publishing Settings -> Unprocessed Plugins