I also enjoyed playing ROTK, but when you said to combine EUII with it, I thought you were heading in a different direction. I definitely don't want character based, and as Johan has clearly said, the player is the soul/essense/etc of the country, not the ruler of the country.
There are alot of other good aspects in that game that can be implemented, particularly the army model as was mentioned above. Food is very important in this time! Famines were very common in the earlier half of this period. These things were not modeled at all in EUII except as random events...
But if they can find a way to model food supply/famine, those are things that have direct causes. They're not random - specific actions such as troops moving through, the kings taxes too high, corrupt bishoprics, weather, many things. So it would greatly improve the realism of the game.