I wonder if Apple will ever add this. Could be via Siri ("make a stop at XXXX" or "navigate to Point A and then to Point B")
As for me, I have never, not once, used waypoints in all my years of using navigation. It was always too complicated to set up, and I have commitment issues with routes.
For me: Navigate to Point A. When I get there: Navigate to Point B. With Siri, this is dead simple. No need to fudge around with addresses on a bad touchscreen (shaking fist at TomTom).