These are a few of my bad ideas. I think they actually have kernels of really cool mechanics in them, but my suggestions would be difficult. Number 2 I would like to see implemented in some way, although I can see it becoming a personal hell for some dwarfs (imagine being a weredwarf if no 2 was implemented). No 6 would result in the world being constantly set on fire.
1) A fleshed out series of laws. Scholars and nobles can propose bills and as your settlement advances, you can get courts or parliaments (depending on laws). Laws can determine a great deal, from methods and the nature of justice (length of punishment, repeat offender status, child immunity etc) to the nature of society. From a liberal society as it currently exists, to one strictly divided between patricians and lesser classes. Patrician, Plebe, Resident, Slave. Grades of each determined by law and debate. Even the nature of the law system should be up to laws and debates, starting with an absolute monarchy. The player has the role of determining what laws get advanced, reading petitions and giving their consent or disapproval. These laws are all encompassing. From who can view artefacts, what people can own etc.Nobles of sufficient rank don't need the players approval to implement laws.
Laws can be set on a civ scale by the mountainhomes and the player has to obey them, ranking up in the fortress mode means getting a wider and more expansive set of control of the law as the fortress becomes more prominent. Civ laws might even allow each Duke to run his fief as a personal kingdom. The player has to petition the mountainhome for national laws at each caravan or even start their own Civ. A French Revolution style event or civil war can trigger if certain conditions are met (laws cause too much unhappiness on the lower orders, nobels feel too sidelined, civs find the mountainhomes too restrictive etc) and the player can find themselves in the middle of it or even having to create a guillotine. All this require maintaining lawyer dwarfs in comfort. Edit: Dwarf fortress should impliment an expanisve proceedually generated litigation system.
2) Dwarfian organ donation and life support.
A chief medical dwarf has to level up to perform certain operations correctly, doing so by dissecting fallen dwarfs and intelligent creatures (men-creatures or captured goblins). Eventually, they learn how to make dwarfian life support with pump mechanisms. This allows a dwarf to stay alive even when multiple body parts are destroyed. After a while and after plenty of research (the ethics and extent of which is a law setting), the dwarfs learn to make advanced artificial limbs and perform organ/limb donation. The register can be maintained and stocked several ways. Through justice, dwarfs can be placed on the register for committing crimes or be sentenced (if serious enough) to be harvested or dissected for research (all executed dwarfs have their bodies donated to medical science). A nobel or patrician can demand a transplant (automatic if needed) and this is performed by the chief medical dwarf (either in the fell mood/ vampire way or randomly picked like failing a mandate). This is from the lower and selects peasants first. A dwarf can be designated to be a prefered organ donor and will be harvested if required. By organs, I mean everything, from eyes to limbs.
3) An expanded class system.
All administrators, their spouses and children and nobles get a patrician modifier. They must have better accommodation than their plebe peers, may petition for raids and other items and have greater demands. The patricians, once enough of a population in a fortress has been reached, will marry only amongst themselves and even demand separate and grader communal spaces. They may even demand personal shires to their personal gods, complain bitterly and throw tantrums if a peasant has better stuff than them etc. Patricians demand finer and better food and booze and get unhappy if they are not treated according to their station. They are treated more gently in justice and get unhappy if they are assigned professions that are bellow them.
4) If a player messes up badly enough, with enough deaths, mismanagement (mass starvation and dehydration) or the dwarfs get unhappy enough, the save will encrypt itself in the background and then permanently kick out the player. This is for humanitarian (dwarfmanitarian?) grounds.
5) A full sex system logged through the sparring screen. Pauses the game if orgasm is achieved with an announcement window.
6) Gunpowder and firearms.
Again, discovered through research. I dislike how hard it is to get fire in the outer-world, so I suggest implementing black powder and firearms. Players, through the alchemists bench, can make bars of gunpowder which makes certain charges. Crafsdwarfs and metalsmiths make shot and siege workshops or gunsmiths make things like cannons, bombards, arquebuses and grenades. These are much more powerful than bows and standard siege equipment, but has the possibility of immolating the dwarf upon firing. Firearms and other such weaponry can be a feature of human sieges. Human seigers can plant large charges which completely destroy a certain amount of grid squares (I suggest 4 in every direction) to gain access to a fortress. They will blast their way into a fortress until the last dwarf is destroyed. Smaller charges can destroy doors. This can also be used by defenders.
7) Have guests in taverns pay for food and lodging with coins. Have nobles demand coins be minted. Don’t actually do anything requiring coins yet (although coins would be a good way to get metal).
9) Re-impliment the economy system, but with fractional reserve banking.
10) Unify the two game modes. The player is an actual dwarf, the expedition leader. The dwarf fortress screen is accessed through their office for planning, but otherwise, its adventure mode. The player can’t switch to the mayor if they’re elected and instead has to make sure they get elected. Its the players responsibility to gain all the items for the initial embark and the first 7 dwarfs. They also need to petition the mountainhome.
11) Implement a gas system based on the fluids system. Certain activities (and dwarfs themselves) produce CO2 and CO. If a fortress isn’t ventilated, the lower levels will become toxic to life and the dwarfs pass out and eventually die. Kitchens, forges etc produce enormous amounts of CO. Players have to install ventilators and built chimneys and advanced ventilation or the dwarfs die in quite shallow mines.