(First post in the forums, BTW. Been lurking forever, and this thread finally convinced me to join.)
I was thinking of something like
Tiberium from the
Command & Conquer universe. A type of rare, valuable crystal that would be found in small (3-4 tile radius) sealed-off geodes. If you found one, it would give you a warning, and the interior of the geode would be revealed without actually mining it. If you decided to continue, you could harvest all of it for a quick profit with little risk, or let it 'grow' on neighboring rock, and keep on making money off of it, albeit at a slower pace. It would be very hazardous to harvest, as it would form on whatever was nearby,
including your Dwarves, if one of them fell asleep on some crystals or something. Also, if you weren't careful or didn't pay attention, it could spread to your fortress and make it uninhabitable. Although if that did happen, you could send in a reclaim party made up of 60 miners and 10 growers/brewers/cooks, and harvest all of it in a few days for massive profit.
It could be limited by only growing on certain kinds of rock, like only the metamorphic stone that made up the bottom four layers of your fortress or so. Or it would only be found far deep down, and not be able to grow up stairways (only up ramps), so there would be ways to keep it contained. Also, it would grow slowly, so you would be able to notice the bright green crystals creeping up your shafts long before they reached any of your Dwarves. To store it safely, you would have to place it on solid metal floors, and not have any stone walls nearby, otherwise it would start to grow on the floors and walls after not being moved for awhile. The crystal itself would be in a shell of very hard unique stone, which would take 5x as long to mine through, so you would have enough time to stop even a legendary miner if you accidentally designated it to be mined.
It would be a very rare occurrence, maybe only 2 or 3 of these geodes per region tile, and it wouldn't show up on the embark screen. If you did find one of the geodes, it would present an interesting decision. You could leave it alone, and avoid mining in the area. You could send in all your legendary miners, and mine it all at once, without much danger. Or you could set up a 'farm' that would slowly continue to generate crystals.
You could build an extensive containment structure around it, with several airlock doors, so it would be safe to harvest. Then, once it was all prepared, you would have mined out a large square around the geode without breaching it, except for one support at the bottom. To breach it, you would then pull the lever, and the geode would fall down and smash open, scattering green crystals everywhere, which would soon start to grow into more Tiberium.
I like the idea of the game being more similar to the 2D version, knowing that you would get plenty of interesting features, but I also like not knowing exactly how your fortress will turn out. Putting in features that you had no way of knowing if they were there would be a good compromise between the two. You could plan out your fortress, and make it precisely how you wanted, but then find a Tiberium geode, and a large pert of your fort would shift downward, and be centered on the Tiberium, and the containment 'airlocks' you built around the designated area. It would help keep the forts away from the rigorous structure of the 2D version, where you had, very little variation in your fort, but still have plenty of interesting features.