Here's mine:
1) I'd like to see a combined religious / language / ethnicity factor for population happiness. The idea would be to keep one kingdom from potentially steam-rolling everyone else.... like what the Spanish, English, and Egyptians have a tendency to do.

Whereas priests and imams could change religion, it would require schools or universities to change a language, and potentially "resettlement" and genocide to create a homogenous ethnicity. And, unlike priests / imams who could spread their message anywhere, you'd have to first occupy a territory before building schools / universities.

Not only would this make the steamroller a little more difficult, but it would also bring a little more realism into the game.

1A) Switching allegiance: If a group of ethnically similar people were unhappy with their current king (such as Swabia and Bavaria with the HRE), in the case of revolt the "rebels" could instead be part of say Switzerland, by proxy, fighting to become a part of Switzerland. Or, if Lithuania shared more with the Polish and Russia overtook them, they would rebel and re-align with the Poles (whether the Poles occupied the territory or not).

2) The pope: If the pope is eliminated, perhaps his rebellions could be a little weaker? Or, he could set up shop in some rebel province close by, or unhappy province close by... if at all. - One of the primary reasons I never played as the Italians or Sicilians was the Pope.... who always came back... again, and again..... and again.....

3) Societal Classes influence unit production: Royalty create knights / swordsmen / et al.... Burghers create Town militia, maybe archers, Basic cavalry, peasants create... well, peasants ~ but perhaps also basic archers, scout cavalry, whatever. The richer a province, the greater the number of royalty. The more trade a province conducts, the more burghers. The rest would be divied up by the peasants.

Also, although there would be "standing armies", which would cost yearly but be of greater morale / experience, conscripted or volunteered armies could either be automatically called up to defend a province, or "purchased".

4) Peasants and other conscripted / volunteered units: Peasants do nothing in an army ~ They attack, hit the enemy, die by the hundreds, and then they flee ~ sending the rest of the army with them. Peasant stats should be beefed up a little, both in terms of morale and in power ~ but to call them up should impact the economy (as in: Full mobilization = 5 years at 50% production, Partial mobilization = 2 years at 50% production).

Peasants and militia would also be used to man the walls during a siege ~ This group would not take part in any land battle, but would instead be part of the "garrison" during any attack. In a sense, they would be part of a standing army, but their sole purpose would be to guard castles or towns, and could not venture out in an offensive role. To see the statistics of a garrison, one would wave the mouse over the castle in question.

5) Secondary forts / keeps: Similar to a castle, these would be used to house soldiers, and in the event of a loss in battle, some soldiers (or many, depending on how many "keeps" are present, could flee here. The benefit would be that, if the primary city / castle was besieged, soldiers from these locations could "sally forth" to engage the enemy from behind. Likewise, they could be assaulted in a similar fashion to that of primary castles (but would be weaker).

6) Roads: Roads would of course be useful for trade, but they would also be useful for troop movement... both to the benefit and to the detriment of the builder.

7) Civil wars / Rebellions: When a civil war happens in a game, one can almost always count on being set back 20 - 30 - 40 years in progress. Perhaps this was realistic, but I think it would be more beneficial to allow capture of a province with minimal damage to the infrastructure... I don't know how, but it's something I would like.

8) Build times: I'd rather have farms and farming (and for that matter, trade houses and ports) be seperate from military improvements. Perhaps there could be an ongoing cost associated with keeping up farms and trade, and if that cost is neglected, over a period of years the production of that farm or trade house or port declines with it. But, if maintained, the farm/tradehouse will prosper and continue to grow. This is different from the "build farm improvement: 80%", which if unhindered, will continue to be at 80% for 100 years or more... it's unreasonable, as throughout history rich regions have become poor, and vice versa. It should be a conscious decision to either build armies or support industry, and limited funds do not always allow for the both.

9) Wonders, and buildings "just for the heck of it": Rather than simply having a "tavern", there should be buildings specifically designed to benefit one class group, or for no other reason at all except to make a civilization all the better? (ex: The Eiffel Tower, Big Ben).

Well, that's it for now....