UnityEngine.GameObject not marked as Serializable?

The serialization is an effort to do a deep copy using binary formatter and memory stream. It works perfect if the item I'm deep copying doesn't contain a reference to a GameObject. When it does, it throws the error that the GameObject is not marked as serializable.

Unity doesn't use the C# serializer. They uses their own serialization method. Most UnityEngine classes have a counterpart in native code. They are more than the managed representation you can see from Mono. Don't mess around with lowlevel stuff when it comes to build in classes of Unity.

They actually sealed all classes so you don't accidentally derive a class from a Unity class. The only classes that can and should be used as base class is MonoBehaviour and ScriptableObject (and the editor classes that are ment to be derived like Editor, EditorWindow, AssetPostprocessor, ...)

If you want to deep copy a UnityEngine.Object derived object, use Instantiate. It works with most objects (i used it already for Materials, Meshes and of course gameobject and components). Keep in mind when you clone a component the owning gameobject is cloned as well along with all components and child objects.