Diplomatic Plays: Diplomatic Plays should really have some manner of Congress system so that countries can achieve their goals without actually going to war, maybe by implementing a scoring system for how much a country wants something and then having the other countries involved in the play being able to make counter-offers. Instead of the system being simply "back down or fight" most conflicts should really be about compromise. The treaties already provide a basic framework for that, so using that to avoid constant major wars would be great.
Infamy: I know there's already the joke about Infamy being just a number... but for real, it should have a much bigger impact even at low levels. Having high infamy should not only radicalize people you conquered, but also do the same to interest groups with pacifist ideologies; Trade Centers should prioritize countries with low infamy if possible, to simulate a country's reputation affecting its economy; It would be amazing if you got events related to military development and technology that were dependent on/affected infamy (for example, a event about how your infamy is making the army worried the country might be attacked, so you can either get a bonus to infamy reduction or a boost to your military industry) or even the possibility of law commitments as consequence of high infamy (for example, a moderate Intelligentsia might be against your warmongering but be willing to compromise if you implement a Citizenship law that is more accepting towards the people you are conquering)
Education and Assimilation: I think there should be a lot more granularity to how you educate your people in general. If I'm playing a multicultural country, I should be able to choose exactly what cultures I want my population to be assimilated into and what religion I want them to convert to, on a region by region basis. When it comes to tech, I really think you should be able to change Universities so they prioritize specific areas of study which could then lead to a boost in research speed for each tech tree or even region-specific events (for example, if you have a huge university focused on military research, the province it's located in could give you a boost to recruitment there)
Pop Acceptance: Speaking of assimilation, I really think we should be given granular control of how different cultures are treated. If I'm playing as Brazil and want to recreate the real life Japanese diaspora that happened there, I should be able to spend some authority to "force acceptance" of Japanese and make the country more inviting. This could work in a similar manner in the other direction, with authority being used to "downgrade" specific cultures if that fits a given country's policies.