One thing that I was really hoping for in Elemental, but was generally lacking in games like Master of Magic, are "dungeons" that have a purpose.  What I mean is, classic dungeons (even in most D&D campaigns) are just convenient smash and grab adventures in which monsters sit around in rooms atop stacks of "treasure," waiting for adventurers to slay them and nab the goodies.  In a way, I'd like to see the classic idea of a "dungeon" be done away with entirely and replaced with more meaningful "hotspots.”  For instance, a tribe of trolls near a run of game; a drake's lair and jealously guarded territory; unhollowed grounds of a recently razed city where the dead now walk; a rogue necromantic channeler expands a tower with his growing army of undead; an abandoned mine, once in rigorous use by a sovereign, now infested with troglodytes.

What's more, I want to see these "dungeons" influence the landscape beyond their front door as well as “emerge” into the world throughout the game.  In a way, they would all be very simplistic AI opponents with simple behavioral algoriths.  So to use the examples above...

A tribe of trolls follows wild game in the wilderness.  Once a sovereigns kingdom expands into their territory, though, they develop a taste for the soft flesh and crunchy bones of pioneers and caravan workers.  If they are allowed to rampage long enough, their numbers may swell, creating splinter tribes and compounding the problem.  If defeated early, they will yield some exotic pelts.  If defeated later, they will yield many of the goodies that they looted themselves, as well as the pelts.  If your kingdom has enough food, you just might be able to feed them enough to sway their loyalty…

A fearsome drake rules over a vast wilderness territory (a territory that contains many sub-dungeons.)  While he may not notice a small party of adventurers sneaking through his territory, he will attack large armies passing through his territory, or budding settlements near his lair, on site.  He adds to his horde any treasure from defeated opponents or monsters in his domian, as well as jewels that he might discover in his expanding lair.  If he isn't dealt with, he will grow larger, bolder, and expand his territory (which may lead to him attacking a sovereign's city should it be in the way.)  If you can storm his lair and defeat him, a sovereign may move his armies throughout the drake's former territory as well as begin harnessing the resources within. 

A large, burgeoning city belonging to a sovereign is razed by another sovereign during a fearsome war.  Given the option to spend resources to give the dead proper burial rites, the channelers decline and leave the city in neglect.  Gradually, the restless dead arise and populate the ruins.  While it isn't a problem initially, by the time one of the sovereigns has won the war and has the opportunity to deal with the problem, the city ruins have become a terrifying necropolis, with undead ghouls carting away villagers from other cities and caravans regularly to swell their ranks.        

A necromantic channeler begins constructing a tower.  At first, he exerts little influence over the landscape, at if he is defeated swiftly, you might gain some mana, some tombs, and some treasure.  If he is left alone too long, peculiar cults begin springing up in nearby cities, and some citizens begin to go missing.  Coincidentally, the Necromancer’s army begins to grow…  

After a city is destroyed/ conquered in a fearsome war, a nearby mine falls into disrepair and disuse.  After a few years, troglodytes tunnel into the mine and set up residence.  If left alone, they may bore throughout the mountain into other mines and become more than mere pests.