It's a rather long story, and I wasn't active on the site at the time so I'm not too knowledgeable about it. But you have to consider how MSE was formed for some context. Basically, the original group of users existed even before MSE. They had a usenet group or something (actually, I think they still do). Essentially all they wanted was a software upgrade. Given the success of MO, they liked the SE engine, but really all they wanted was a stable platform for asking and answering math questions which was more advanced than Usenet.