Yeah--Why does it matter that the registry is endian-specific? Doesn't Windows only run on little-endian processors (x86, x86-64) or am I mistaken?
Is there any reason why a new version of Windows couldn't do away with the registry and create a layer of abstraction to allow programs in a "compatibility mode" to run normally but have its registry interactions translated to the new system? Wouldn't that be a similar principle to what Wine does?