Okay, I guess I should start because I am the one posting the questions.

Some improvements that I do enjoy better is of the following.
1. No Civil Wars or Massive Rebellions that I know about
2. Graphics, but this is a no brainer.
3. Seige Engines, I never really played RTW so I can't comment on it.
4. Building Build times are now reasonable, for a fortress in the previous MTW game, it took 20 years, now its more realistic.
5. Archers and Artillery are more effective now.
6. Different formations and special attacks in common units like Scilltron for spearmen.
7. Even knowing that Alliances are still a little off, I feel that they are better.
8. To move my troops onto someone elses land without it being a formal attack or break alliances to do so.
9. Pope feels like he has more power to me.
10. Artillery is more than just one "Engine" to a unit.

I have some more to add later but I kinda want to see what others post first.