Hi.
I've read many reviews/threads complaining about the game as it is. I must confess there are many things I don't like either. But there is one thing I do like : modding. I mean, we can complain about balancing, suggest features or ask for others to be removed. Or we can mod it the way we want to play it !
Here is what I personaly would love to make :

I would have the champion and sovereign aspects of the game separated. I mean, the game already lets you focus on one aspect in particular if you want, but I think you are disadvantaged if you chose never to found a city or never to wander the wilds. Some could be sovereigns, found cities and manage empires, while others could be champions, visiting dunjons and all. Both could interact : sovereigns could give rewarded quests, which could be picked by champions in the tavern, for instance : ridding of bandits, spying at the ennemy kingdom, escort caravans, rid of another champion, set free a kidnapped offspring, ... Champions could even join a kingdom (because they like the kingdom's policy, or for money) and participate to battles. The sovereign would command the regular armies, while champions would control their own character and summons.

- Interactions between cities and champions could be managed through buildings : a tavern would allow the sovereign to offer quests. A range of shops would allow the champions to buy stuff (potions at the herborist, weapons and amors at the armory, bows at the bowyer, leather armors at the tanner, ...) and the items for sale in each building would depend on the resources available in the city. A library would allow champions to buy/learn new spells, etc. An inn would let the champions rest (and regenerate HP/MP), etc. The sovereign could set taxes that influence the prices of items and services for champions, and that would let him have some money from it.

- I would have resources be "per city" to make trade and caravans more important (and hence allow caravans to be pillaged ). A caravan would have a "cargo capacity", you could fill them with any resources you want and then send them another of your cities, or to a foreign city you have a trading treaty with to sell them there. These caravans could be automated. Resources would determine what buildings and troops you can make, but also what items you can sell to champions. I know it would require a lot of "micro management" but, remember the sovereig would focus on city management and armies

- Champions could be three main classes : mage / rogue / warrior (but each champion could be very different depending on his stuff, chosen spells, special abilities, stats, ...) The ccharacter class would limit the equipment the champion can chose from. A mage would obviously cast spells, for his own benefit (like a necromancer), peoples' (a priest or an enchanter), armies' (battle mage), nature's (druid), ... A rogue could be a bandit and steal money from city treasure, pillage caravans, ... he could be a spy and get invisible to most units in order to get intel ot to sabotage buildings, or he could be an assassin : good in one on one combat because of his skills (poisons, invisibility, traps, ...). The warrior would be good at combat, able to deal and take huge damage. He could also have a range of combat bonus for the troops that fight with him and he would be the one able to equip the best weapons and armors and he could train/recruit soldiers (like a private army, mercenaries for instance). 
- Sovereigns could have bonus enchancing cities (like 20% gold bonus, food, prestige, construction, ...) but these would take effect only in the city they are in charge of. For other cities, they could name their children governors to have bonuses there too. They could get old and die, and without successor, they would lose game. Sovereigns and their dynasties would be units in tactical map (like they currently are) but could not take part to battles. They could be murdered by assassins, or kidnapped for a ransom (more difficult, if not impossible while inside guarded cities), and when their city would be taken, the invader could chose to imprison them, set them free or have them killed. When a sovereign loses, if he married children to foreigners, these could claim the remains of the lsot empire, cities or gold for instance, depending on the place in the line of succession of the child. Marriage would then be mostly a matter of survival (as you would need to constantly have a successor) and a very heavy diplomatic matter (you wouldn't trade your children lightly). 

- Why not, if you want "shared empire control" let one of your governor offsprings become "playable" by someone else (a friend for instance) as a vassal (if your empire grows too big ). The vassal would be a sovereign too, able to marry, build new cities, trade, train armies etc. but would not have diplomacy until he (maybe) declares independance. He would for instance be at war with the ennemies of his lord, have to pay taxes to his lord, etc. 

- Persistant maps ? A champion would lose the game when he would die. A sovereign when he would die without a successor. But any of them could restart from the begining on the same map. Cities could rise and fall, be invaded and rased, reconquered and rebuilt. Why not all on the same map over long periods of time ? When they grow bored of the game sovereigns could resign (their kingdoms would be AI driven or taken by another player, for instance a vassal or a foreign sovereign who's lineage has been mixed with at some point) and champions retire and give all their belongings to someone or lock it into their "home base" (tower, fortress etc.) for other champions to explore . They could then come the day after and see how the world changed. If nobody took control of their cities (or destroyed it) or pillages their "home base" they could play it again, else they's have to restart.

- Goodies : well they would need to change especially if the world was to be persistent. But "places of interest" could be suitable. There could be monsters lairs spawning in the wilds (areas outside sovereign's borders), champions could build their "home" : tower of sorcery, bandit secret campement, etc. which would be required for unique abilities : you might need a specific mage tower to cast the highest level spells, a bandit camp to kidnap people, a fortress to train mercenaries (warrior), ... which could of course be razed by sovereign armies or other champions. There could also be other places of interst which control would provide bonuses wether to champions or sovereigns, or both. 

- I would of course have tactical battles involve more than one player (up to two sovereign armies (more could be fun too) and as many champions as you want).

- No tech trees, or only warfare and civ ones (with many changes) for sovereigns. I don't like the fact that you can chose between a few available techs on breakthrough. I'd rather have fully chosen techs (like civ4 for instance) or fully random ones (you have a random tech in the selected tree, you only chose the tree ). 

- A mage champion could learn spells from the spellbooks he owns assuming he has access to a city library or a tower of his own, which quality would determine the speed of the research. He could get new spellbooks exploring places of interest (towers abandonned by other mages, evil temples, etc.), copying them from other mages (like trade between two mage champions), or learning them in cities. He could sell any known spellbook to a city library, where any mage could then learn it. 

- In addition to specific places (twers or temples), it could be interesting to make "required reagent" necessary for some powerful spells (getting them becoming a quest warriors and rogues could participate in, or even sovereigns coudl try to get them through harvesting or trading).

- Turns would need to be simultaneous and have a limited duration

>> I'm not sure it's even possible (supported by the engine) and I'm sure it would take ages to mod. I'm not sure I would have much time left by my class, and I'm sure I couldn't do it alone ! Anyway if there are people who would and could help, contact me (at this point, this is a mere "idea", not even a project yet).