SS1 was conceived by one of the most creative designers in aviation as a point solution for the X-Prize contest - the minimal design/implementation to precisely solve that problem in the most cost effective way possible (as detailed in "Test Gods").
This cobbled together, even borderline, solution was reimplemented as a revenue producing, passenger joyride vehicle, without a lot of (apparent) deep understanding of the real problem and the quirks of their existing "solution".
Pretty much, SS2 is Branson and droogs saying, "SS1 is great, just blow it up and start printing money".