As it stands I can generally generate a world, pick a site with no real searching, and build a fortress that can produce anything and everything I could ever want, which makes caravans almost completely unneeded. Instead, what if you made everything much more scarce in general, and then scattered some sites around in world gen with certain resources being very abundant? You’d follow your geology patterns and so forth, so maybe a “site” might include a mountain range, but it’d be confined to certain areas instead of everywhere. Players would have to be alerted to this before embarking, and would have to be able to search for it in the site finder to make this fun, of course; a guess and check approach would be disastrous.
Even though iron is one of the most common metals, you can’t just go anywhere on Earth and plop down an iron mine. You might be able to find iron in most areas if you look hard enough, but it’s not economically worth mining there. Unfortunately, in Dwarf Fortress, the idea of a mine doesn’t even exist; you don’t settle a site for mineral abundance, you settle it and assume there will be minerals present, the only choice being looking for sedimentary rock where metals are more common. Changing mineral abundance levels on a local and global scale would fix this. Along with value rebalancing, this change would greatly increase the fun and challenge of the game, and would make a number of neat features possible that could make the game come much more alive. Here are some of the ways I can think of.
You might start a fort specifically to mine one mineral. Maybe you’d start a dwarven diamond mine in the middle of a desert, with very little of value around you. No trees, no water for farming or drinking (or booze production if it ever requires water), and little mineral abundance below you. All you’ve got are tons and tons of diamonds (and assorted gems that are associated with diamond-rich areas). You rely entirely on the caravans for everything, and as the game grows, might have to send out patrols to protect the caravan routes or destroy nearby bandit camps, etc. And so you rely on your gem industry, as well as exporting raw gems if needed. There might need to be some sort of balance issues to address; you might add in size and quality for gems, which would make it so that you’d have to sort through a lot of gems to find any that would make it profitable. But on the other hand, you’d have tons of gems available on site to mine through, rather than a small handful. Still, it should be exciting when you find a high quality gem, because you know it's worth a lot, and the value actually means something strategy-wise, unlike the current game. Taking this one step further, why not introduce extremely rare artifact-level gems, like the Arkenstone from The Hobbit, or the Hope Diamond, etc.?
You should be able to have a mining outpost with vast quantities of the more valuable/strategic resources, and have it be profitable on that alone, or at least in part. It’d also add a bit of depth to the game, and make things like mine carts more useful; instead of small veins here and there scattered across the map, you’d be following much larger veins that would encompass your entire mining operation for decades or more, so it’d be worth installing the mine tracks and so forth; you’d be hauling large quantities of material out of the mountain to be smelted, or sold as coal, and it’d all be in lines following the vein. This might require some of the realistic mining suggestions from the eternal voting so that you don’t just mine everything in the first year, but it’d improve the dynamic of the game a lot. If you want to balance quick digging for establishing a fort with slow digging for establishing a mine, maybe make it so that ore squares produce a lot of rubble that has to be cleared out before the next square can be dug, and mine carts can only hold so much; essentially you’d be sending a mine cart back and forth a few times before being able to mine deeper. This could also address how dwarves can carry huge boulder with no trouble; instead break up ore boulders into more manageable chunks, which can then be loaded in the cart or carried out by hand if necessary.
In order to rebalance values and the new abundance of metals in certain sites, you might need to change how metal ores and bars work. It makes sense to get an iron bar from a boulder of iron ore, but not from gold, silver, platinum, etc; gold ore contains very little actual gold, though it might have some silver or copper in with it (the largest gold producing mine in the world is actually a copper mine). Instead for some of these ores, change what you get from them to nuggets, and make it so that you need 20 or so nuggets to smelt a bar; number of nuggets might depend on the value of the site, how close they are to the main part of the vein, or luck. Adding nuggets means you can also add in gold/gem panning in rivers and streams downstream from their sites, which would be fun; even an adventurer could do that. All this means a precious metal bar should be worth a lot more and is harder to produce, but you should also be able to get a lot of use out of one bar. There’s already a quantity system in place for bars and thread, so why not use it. Make 50 rings from one bar, or use it to gild a bunch of copper statues with gold, or the walls of your dining room. Or take several gold bars and make a solid-gold throne, fit for a king. Hell, you could even have the construction of a royal throne be like making an artifact, only without the mood. Requires XX gold bars, X diamonds, X rubies or sapphires, X dyed cloth for the cushions, etc. , possibly modified by ruler preference. Putting it (or something like it) together might be a demand from a noble, or a requirement for a king to show up, etc., and would automatically be artifact quality. As it is now, solid gold items aren’t really significant in any way, when something solid gold should really be something special.
The presence of mineral rich mines would mean there are going to be more bars produced for import and export, so this gives an opportunity to increase the number of bars needed to produce things, which can make metals more valuable since you’d be multiplying the number of bars in cost to produce. The game used to work this way, but now everything takes a bar, except goblets which take 1/3 of a bar. Increase it again; you should need a number of bars to produce a quite a few bars of steel to produce a full suit of armor, and a LOT of bars to produce a life-sized, solid metal statue of a dwarf. This would work better once caravans are established that can provide plenty of bars if you can afford them, rather than just a few as it is now. This gives a use for common metals like copper; instead of being a relatively worthless copper statue requiring a single bar, you now have a large statue worth quite a bit requiring lots of bars, and you can then gold-plate it afterward (or other metals, but I don’t know if much plating beyond gilding was done during the game’s time frame). If you go this way, make sure you adjust the learning rate to go with it. The more bars it takes to make, the more time it takes and the fewer you can make.
If you really wanted to get into it, you could change the metals to have a happiness value associated with appearance rather than value to make gold plating common: “Admired a beautiful gold statue” vs. “Admired a copper statue” even though the gold used in plating it might not increase the value of the statue significantly. This could also make certain alloys more valuable; making rose gold might not be profitable for trading, but if you don’t have much gold, you can make the alloy and still get high-rated thoughts while stretching your gold supply. Of course, not having access to everything makes whatever metals you do have more useful in any event.
All these changes improve gameplay, but simply changing the abundance of minerals opens up a lot of cool situations. Once you have sites supplying resources, and sites using resources, you can set up trade routes, with caravans coming and going between sites on routes. Bandits can then start ambushing caravans, causing problems on both sides while profiting themselves. This might force the civilization to establish a fort to protect the caravan route. Once established, caravans now have another stop on the trade route, making it more profitable and increasing trade. The trade and security might draw in settlers to the area, and a town might pop up around the fort. Then, a hundred years later, the mine dries up and the main reason for the caravan no longer exists. Without the caravan, the need for the military goes down, and eventually starts moving out. Eventually, the fort is abandoned and people leave the town, and you’ve got a ghost town, where monsters, bandits, or kobolds might move into.
One thing you could also add would be the whole coal miner black lung problem, if coal mines were specifically set up to mine coal rather than every fort mining coal. A coal mining fort might be kind of fun, because you'd be dealing with tons of dwarves getting sick over the years, and rotating them out and so forth; ultimately, it'd be a harsh work environment and would be interesting for play.
Ultimately, I think changing resource abundance from global to local would be a great path for the game that would lead to greatly improved gameplay and mechanics.