The more I think about it the more I think these two things are important to a game of this age, and I am hoping we get confirmation on whether they will be included soon.

Morale:  Combat up until the modern era chiefly consisted of two armies coming together until one of them broke and ran.  Most games do not represent this, and instead have their armies unrealistically fighting to the death, however the real trick of Medieval and Ancient warfare was not to kill all of the enemy but to break them, causing them to run.  That is how specialized super-units like the heavily armored knight or the viking berserker acquired capabilities all out of proportion to their numbers.  This would be especially important with creatures like dragons and other super units... a creature that would cause panic among lesser soldiers, and whom only the most elite troops could stand up to would accurately represent the power of such animals and the difficulty that an empire consisting largely of humans would have confronting them.

Water:  During the medieval and ancient time periods the only efficient way to move bulk goods was via water.  Control of the water enabled food, stone and manufactured goods to be transported en masse, and dramatically influenced just how large and powerful cities could get.  All major cities in Europe were either on the water, or connected to the water, and large seagirt cities like Byzantium could not be successfully besieged until their sea lines had been cut.  Therefore I hope that at the very least a naval system is included in the game, and hopefully the advantages of being on the water are represented.

edit:

Actually, I think I've got an idea of how to model morale.  Each time a unit takes damage it makes a morale check against a value that is determined by the amount of time spent in training/the experience of the unit.  The more damage inflicted on the unit in a brief time the more penalties go into the morale check.  For example, a heavy cavalry charge into a unit of lightly armed, poorly trained peasants kills 10% of them in a go, in addition to a shock effect (for the larger size of the unit, and probably a charge bonus for cavalry... if it was a dragon it would have a significant fear bonus against regular units).  So while only 10% of the unit is killed (normally cavalry charges themselves didn't actually kill that many... but the shock effect would shatter enemy lines), the poorly trained and equipped peasants break and run, and are then mopped up unless they can be protected long enough to rally (the chance of which could be determined by the leaders or heroes you have on the field, and where they are located).

That way hastily trained but well equipped troops will have difficulties standing up to well trained battle hardened troops with similar armaments (as was the case in history).