Maybe you have different goals than us. You're trying to build communities... we're trying to make the Internet a better place to get expert answers.
If it is the case, I think this is the fundamental tension: You've built software geared to rating and creating answers, but to get those answers you need vibrant communities -- and the resulting software is so complex and strictured it is effectively anti-community.
Take Wikipedia as an example. Community is necessary but it is not the goal. The goal is encyclopaedia making. Most online communities do not produce a wikipedia.
What this adds up to, in theory, is sacrificing some community building ability (more sites will dies from under participation)for more Q&A ability. While more of the remaining will produce a good archive of useful answers.
*This doesn't directly answer your original claim that the software is good for SO specifically but cannot be widely applied. But, if what I suggest is true, then you would expect it to appear that way.