I can see your point. I just think the same could be achieved with everything together. Questions could be assigned a category. Each category could have it's own associated css style and simple URL to give it a uniqueness. Also user reputation could be calculated on a per-category basis in addition to a site wide basis. You would end up with little kingdoms and little kings, while keeping it all together.

Just an idea.

But with the community process of the different Stacks I have a feeling there are reasons other than technical for the separation.