An inability to easily conquer (or even get CB on) small islands next to your land. (Now any two provinces that share a common seazone are adjacent.) The relations system being in a way that there are only +200, +100 and -200 relations. Cascading alliances. The unneccessarily complex technology cost curve, that ensures that small nations can keep up. The woefully outdated and abusable Centres of Trade system. The fact that some initially big nations can be balkanized to no bigger than 3-province minors, while others are not so unlucky. The fact that if you are big, you won't be ganged up on, because everyone is happy that they are not next. Related, the fact that if you hover on infamy limit times 0.999, nobody notices how you grew three times your size in ten years. Hell, even the fact that the start date, 1399.10.14 may as well be the single least important date in world history. The words "any day now". (The siege system didn't change, but now, you are informed of how it works, and how any given siege goes). The fact that the Japanese and Chinese AI aren't prepared for Divine Wind gameplay in their areas. The papal system is improved a lot, and now the three western Christian religions are pretty much balanced.
And these are only the big ones. With every dev diary (and I followed them religiously), some change that was made made me very happy.
I can only recommend EU4, even against the fear that I'll be called "just another fanboy".