First off, I want to say I love DF for its freeform nature. But sometimes, I feel directionless and daunted by the sheer variety of ways I can channel my dwarves. What do I want to optimize in my fortress?
So - goal-based DF. It's in the same spirit of challenge games, but the way I'm thinking of is more "connected" to the world. Rather than just imposing restrictions purely to make the game harder, each fort would have an assignment handed out from the king. Some would come with pre-selected loadouts, others could offer some more freedom in that area, and the success (or failure) of that challenge can have a world-effect.
I'm just tossing ideas out here.
1. Refugees. An army is marching to lay siege on a dwarven city - and you've been tasked with providing for the refugees. Build a fortress capable of housing, feeding, and defending 200 refugees.
2. Stealth. You've been tasked with creating a hidden outpost close to a goblin lair. Impact the outside site as minimally as possible - dig down right away, deconstruct the wagon ASAP. No building outside or even going outside.
3. Shrine. You've been tasked with designing a temple to some dwarven god. Aesthetics count - the king will be very disappointed if there's no domed ceilings carved with frescoes.
4. The Great Brewery. Disaster has struck the kingdom - a !!suspicious peasant!! made it into the greatest brewery of the empire, and as a result the whole thing burned down and exploded roughly simultaneously. No time for weeping - you've been chosen to create its successor. Construct a fort dedicated to the production of alcohol - of as many varieties as possible, not just wine, ale, beer and rum.
5. Diplomacy. Five courtiers of the king's court made some ill-advised remarks within earshot of the king, and as a result have been ordered to go and found an outpost. They've hired you and one other dwarf at exorbitant prices (they'd have to be) to make sure they survive. (The five nobles only have social skills and refuse to do any work that is beneath them. Make sure they survive for x years, after which it's safe for them to return to the courts.)
6. Wealth. Pretty simple - the kingdom's coffers need lining, so hop to! Found a fort and start accumulating wealth as fast as possible.
7. Artifact. There's rumors to the effect that a haunted locale was once home to a item of great importance. Groups have gone in before (and never returned, of course), but never one so dedicated as yours - you're staying until you have that artifact! (Found a fort in a haunted/terrifying location and survive until a dwarf successfully crafts an artifact via possession. Then get the hell out.)
8. Assassination. Your group of seven has been chosen to assault a goblin fortress - and you're not getting any backup. (Turn off immigration.) Slay the leader (the hardest-to-reach goblin) and escape within x years. (Caveat: No sapper-style undermining. Melee is where it's at.)
Obviously these are all very formative, but I think "flavored" challenge games like this, as part of a cohesive world and with a clear goal, could be a very fun project.