I think it would be interesting to see an expansion on the dynasty system as well. Ever since the early days with the early Civ games I always thought it a bit odd how you are a leader that lives thousands of years and despite having changes in governmental bodies, such as going from dictatorship to a republic, you still remain in complete control. That's not really a change in government that's just a change in what people focus working on (aka bonus/penalties). 
So instead I've always preferred to consider your role in such as the shadow government that lots of conspiracy theorist believe exist and have been the ones "really" running things for hundreds if not thousands of years. If you pretend that your that group then playing games like Civ makes much more sense. hehe
Anyhow more to the point I always thought it would be interesting to have some kind of dynasty system where you did have children and you could then appoint those children to take over once you passed on. The game would still remain in your control obviously but those children may have personality differences which translate into different bonuses like they do in Civ currently.
This could potential add a whole new slew of options such as assassinations. Thus if your leader is killed with no heir to the throne then one of the siblings become ruler. But more interesting is the potential for strife and in fighting which was common in medieval times. For example if when you do pass away and unhappiness is High you will still get to pick which ruler you want to take over but some of the other children being less then thrilled at getting nothing will seize the chance to stage a rebellion in which some cities will fall under their sway. Thus breaking off and forming new nation which you will then need to deal with. And of course the marriage thing can be used to help "merge" nations together in the same regard.
This would add a whole new depth to the game as whole sections of land and cities can change hands without any military action. There was a Civ4 mod that did kind of do this called RevolutionDCM as I recall. It's added the concept of "instability" to the game which was the larger your empire got the higher the instability became until cities would revolt and form new Civs. I thought it was a great mechanic as it really helped keep Civ size in line early game so some lucky guy in an open area by themselves didn't expand real quick and get like 2x the cities as everyone else. Or overly aggressive Civs don't steam roll a few small civs near them at the start and end up with 2x the forces then go on to steam roll everyone else. It really made it hard to maintain a large empire much more then the whole increased maintenance thing ever did. But at the same time I've actually had really small civs near me ask to merge with mine and I got all their cities and units. Though that was rare and the cities wanting to break away is more common.
But the fact that your children might fight over who gets what when you die does add a whole new dynamic. Especially since the concept of revolts is handled rather loosely in most strategy games. The threat and consequences of a revolt should potential be as bad as invasion from another empire. After all governments often fell or lost control of large sections of land they use to control during revolutions. They were as costly and deadly as many war. Yet most games treat them as modern day protesters on strike. Instead of how they were originally often by execution to put down the instigators unless it was a full blow uprising which gave rise to military action.
Well I don't know what's coming down the road for the dynasty system but right now it just seems like a hero breeding tool. I think it would be much more interesting if you did assign your children to rule over different sections of the empire and thus they gave bonuses/penalties to the cities they over saw. This would really open the odd for some interesting stuff especially on larger maps. Cause on of the things with larger maps is you almost need some element undermining the growth size of an empire. Maintenance penalties rarely do it and ultimately do little to slow a true economic focused player such as myself. They just tend to cripple players who aren't good at maximizing their economy.
