Very detailed analysis. I agree with the claim that "fewer stops, faster service" on the surface. However we'd have to see if that's truly the case, as cities have red lights and traffic, so the bus stops anyway ... I believe, taking this into account, the difference might not be that significant.
Two problems - for one, riders entering and exiting takes time, especially if the public transit scheme says you can only enter at the front and have to show/buy tickets at the driver, and the other problem is that in most areas, buses cannot request a green light, so with a loop time of 1-2 minutes (quite common in German cities on busy roads) you may easily lose 2-3 minutes in the worst case just from a mismatch of departure with the light being green.
And over the course of a few stops, that lost time can add up quickly.