Okay here are some things I would like to see:
1. The ability to arrange for a marriage for your children before they come of age.
In real life marriages were often contracted between the nobility years in advance. A well-known example from the height of the time-frame was Henry II and his sons. Richard was contracted to Alys of France when they were both not yet teenagers (he was 12, she was 8). And there are many examples of even younger contracts. In addition there should be a option to break the contract at any time by either side.
2. More in-depth court and vassal relations
While the original CK was a wonderful game the court and vassal interactions were generally flat. I would love to see a more in-depth and better fleshed out court. The same with vassals and how the ruler interacts with them, as well as in turn how you as a vassal can interact with your ruler.
I would add that I would include under this heading that I would like to see better interactions between vassals themselves. The ability to create factions would be good.
3. Better Diplomacy
Contrary to popular belief medieval diplomacy was hardly flat or simple. This was a flaw in the original CK and I would love to see this fleshed out more. Many historical diplomatic maneuvers from the era were not replicable in CK, which is a shame. Alliances were a joke in CK, and I would consider fixing that a priority.
I would add that I would include under this heading better interaction between dynastic branches, and some concept of seniority in family. The ability for the eldest, or most powerful, male in the dynasty to be able to dictate to other members of his dynasty would be good.
4. Better War System
The existing war system is not very good. This needs a major overhaul, and some serious depth. Perhaps more then anything, creating a good war system and better diplomacy would integral.
5. A more accurate representation of the Holy Roman and Byzantine Empires
Both of these empires were pretty poorly represented in the original Crusader Kings as the feudal system used did not fit the realities of how things worked in either empire. I would like to see a better representation of both in CK2. The Holy Roman Empire would probably not be too difficult, except for the election system. The Byzantines would probably require a bit more work, but given the rising interest in them it would be more then worth it.