I'm not really sure what the problem is here, it was nerfed because of the portential to crazily stack bonuses, and that's a good thing. It really doesn't matter how important stone was in the Ancient World in contrast to other materials either, what we have is an system in a game to represent building tech. It's an abstracted system, in a game. As long as it has some Historical relevance and accuracy and is balanced, that's really all that matters.
Now here's a system that is crazily unbalanced and makes no sense - seeking treatment at 200 Gold a pop...in what universe is that realistic or balanced? that's almost the cost of of TWO FORTS in my current play-through....