Surely you have to build communities to do this, though? Your earlier answer mentioned how you needed voting so the "community" could choose best answers, you needed tags to keep sub-communities separate and so on. And one of the rating criteria for the new SE sites seems to be how much of a community they manage to create.
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.
I'm siding with spolsky here. The ultimate goal you have in mind is defining. Since building a community is hard and is the hurdle that kills most attempts, people will often see it as the goal. In many cases, it might be the goal.
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.
I think your reading to much into this. To me it seems like the stack exchange sites just got too little traffic to reach critical mass. Ask Metafilter is an exception to a lot of other communities which became awful as they grew.
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.