I know Toady is planning on making generated fortresses feel more playerish, but I don't know if he has a plan for how to do it. If he doesn't, here is mine...
He could create a module for every type of industry, building, room, etc. These modules would be probably 24x24 squares in size, and they would be designed to fit together seamlessly. This way fortresses can have a more realistic feel, without it having to follow a strict set of rules. Perhaps he could have meta-modules also, which would contain several related modules, but still randomly placed within. Perhaps he could include a module editor, which allows players to create their own modules, perhaps to their own advantage for adventure mode.
Contained within the modules would be: workshops, stockpiles, furniture, engravings, precious metals/gems, weapon racks, armor racks, artifacts etc. Of course a Kings module would contain the engravings, precious objects, artifacts and the like. Whereas a blacksmith module would contain weapons, a forge, an anvil, and typical blacksmith things. Thinking bigger, a meta-module for Metal Industry could contain, a blacksmith, a smelter, a furnace, a specialized weaponsmith module, etc.
Seeing as generated fortresses have limitless resources, you could really give it an uber-realistic feel by putting hammers and water buckets in the blacksmith, scepters in the kings room. You know, all the stuff us players are too lazy to do most the time.
Any further suggestions/ thoughts?