I think the real problem is that Microsoft hasn't place enough focus on getting the Settings app correct from a UI/UX perspective like Apple did with their Settings app. There's nothing technical preventing them from offering a streamlined experience in Settings that allows you to easily configure advanced settings when necessary. It's just design effort on their part.
If they can get their Settings app to the point where nobody wants to use Control Panel anymore, then that's the right time to deprecate it.