Hear hear GW!
If I really let myself go nuts I would love to see the abililty to implement complete government types - not talking abstracted "bonus this or negative that" but say in EWOM it would be cool to be able to groom your offspring to be somewhat independent minded city/state rulers - obedient to you but yet with their own personalities that they would try to accomplish what you want but THEIR way.
It would be great if you could in one game set up an heir that was pretty much a totalatarian subject only to you, in another game set up a council that ALL of your heirs would participate in (more ideas but also slower to act due to bureacracy and power plays, etc.
I would like to see a breeding system with a whole host of attributes and varying degrees within each attribute that you could fiddle with.
I would love to have to be torn between the choice of sending a heroic descendant out to fight but be torn because i also did not want to endanger his genes for the next round of the breeding program.
I'm not as big on the black ops/spymaster aspect, but I wish for those that did that there was an in depth spymasters desk.
I wish that every single resource in the game was a finite unit that you could either micromanage it from the point that it came out of the groun until it ended up in the trash heap, but also that you could let "market forces" move around as needed and that you could micro as much or as little as you wanted.
And about twenty other things. But I am honest enough to say that a game like this that had the amount of depth in all areas that I would like would probably be played and loved by maybe a few hundred people at best, and at worst even though I love the idea, I might hate the reality.