Trade:
I dont know if this is possible but I would like trade nodes that are not exactly dynamic but at least movable to some degree, depending on the trade power of the nation, a powerful trade nation should be able to significantly able to change the pre-set direction of the trade line.
In addition, I would also like to see the rivers used for trade, for example a trade network passing through Danube,Mississippi,Nile and so on would be great, I think that's something everyone would like to see. To expand on that, even moving naval units through rivers should be possible, such mechanics could be greatly beneficial for the game, but only if it's made so that they dont become 'gamey'.
One aspect of trade that has, as I feel, been left out is the Slave trade. Honestly I am not sure how paradox can make slave trade much more interesting and engaging but I am sure there are quite a few idea out there, such a significant part of history should be represented better.
Characters and Dynasty:
Unlike some of my other fellow players, I truly think that EU4 deserves more special and specific characters, just a name and three stats do not satisfy my personal experience, I would enjoy different character portraits for rulers, more obvious dynastic ties(a way to see which dynasty the character comes from) and maybe you can even educate your heir in the fields of diplomacy,administration or military. Now, I dont want to be understood wrong, I do not want a CK3, just some much deserved and needed flavor to the characters in game. This would make pretenders and revolutions much more interesting. I mean dynasties and a ruler's education were important factors in EU4's time-frame, so why not try to add a little bit more flavor to such a aspect?
Colonization:
Although colonization is somewhat fun in EU3 there is not much that you can do, in my opinion. Hopefully in EU4 this will be changed with the whole new trade system. I think the Dev's should find a way to make colonization more interesting, for instance individuals could(colonial man or conquistadors) play a big role in colonization, or simply the colonization system should be changed overall, I dont have very specific ideas about colonization but I am definitely for changing the current system.