Well, im pretty sure there won't be any city happiness in the game (otherwise I would have used that as a variable in my ideas), however other potrayals of Social Discord, Civil Strife (royals revolt), and Extra-planar invasions would be nice.
Usually, however, each person creates their own clock, and the end of the game is a battle of the Giant Clocks. That is sometimes fun. Perhaps boring for singleplayer, but in multiplayer it can be a blast. Sometimes in games I want to build palisades and walls for that "Just in Case" they ever get attacked, but usually I should know that they never will get attacked.
Once you have enough cities, nothing ever usually attacks the inner cities. Perhaps we could have raoming bandits/ bandit armies, and neutral trolls/ect, which can move in-between our cities (towards the inner cities) and occasionally attack an inner city. Say there is something special about inner city X which is attracting a bandit army or a troll. Then those creatures, which might normally only roam the countryside, would actually lay seige/attack the inhabitants of the city.
Another example, a disgruntled Royal raises an army in the countryside and marches onto an Inner City to start his powerbase. Maybe the disgruntled royal gains a few external, outlying settlements as "his cities" ... of course if he is first born, or a particularly powerful Royal .... he could rise with half of your empire already under his command. The question I raise, is how would your first born end up being so mad??
Well, I'd like to think that each Champion (especially Royal) has a personality. Some Champions get increased Loyalty from your Channeler doing evil things, and some have an opposite effect. Some Champs get increased Loyalty for your actions to be Chaotic and Outside social norms, and others are opposite. Some Champions are Xenophobic, and others are Xenophillic. Some want a salary of more gold, others want a salary of more prestige/land/better city.
In this way, you would know which Champions to throw to the wayside, and which champions to coddle and support. I think giving in to their needs could, in some cases, increase their experience points/ level them up. And then some cases of particular disfavor could cause them to either Desert (NPC champ), or begin a Revolt (Royal Champ) by raising an army.
Executing a Champion would, of course, lower the loyalty of all but the most depraved champions, unless that Champion has led a revolt. If a champion raises an army in revolt, you can capture him and execute him without reprecussions (in fact it will increase the loyalty of al champions, if only temporarily) because he commited treason.
There are a few events in FFH where a building burns down, or a road collapses, where you would either pay to get it replaced/repaired immediately, or have to go through the trouble of building it over again. Also, in some cases you needed a Particular Magical Node in order to choose the "best outcome" for a random upkeep event. For instance, Muris Clans dumping waste, or disease hitting a city. I think disease could be spread along trade routes, and it being a Temporary buiding, which takes up no space, that adds a certain amount of negative prestige. You can take magical intervention to combat the disease more swiftly, or use mundane methods of the time to slow its spread and decrease its effectiveness. If no measures are taken the disease increases (greater decrease in prestige) until your city could possibly grow to a very low number. A city won't go below a certain amount, but if a disease is still quite strong at a low population, the negative prestige won't grow any further (or maybe it will) but it won't decrease either. Once the disease starts to be fought in some way, the temporary building's negative modifier will slowly decrease, until it is little noticable, and then decreases altogether. Living units in a city with disease ... thats a tricky one. Should your units die? Personally I think that they should be effected by the level of disease. Minor disease, and all units HP 75%, More Disease, and all units HP 40%. Powerful Disease, and all units HP 10%. however that route seems a little simplistic. I think instead the total hitpoints for the entire army should be placed on an array, and for a minor disease, each turn has an X percent chance of an HP being removed. Medium disease every turn has an X percent of 3 HP being removed, and Great Disease an X chance of 5 HP being removed each turn (5 chances for an HP to be removed). In this case, high HP units could be weakened, and low HP units would straight up die. I rather like this idea better. Some units, like undead, demon, Edar, Umberdroth, and Dragon, could be immune to disease, and therefore not be included in the array.
There could be a random event more inclined towards "older" buildings ... a building that has not upgraded in 20 turns or more, to be "wearing down" and need to be paid to be replaced, or rebuilt. It would be bad for buildings to be popping up every turn, so use some Algorythm which emphasizes that only one of such buildings could wear down per city per 5 turns. And even then, not always. If a city does not have a governor, or has poor/evil management, this chance could be higher. If it has great management, this chance could be lower. I'd say a 1 in 20 chance within the framework of once per 5 turns after initial 20 turns. Upgrading a building resets the counter.
// although this could all be far too complex, including the posts above me. I would rather have one good game than five great games competing against each other.