1) Allow diplomatic intercession in wars between neighbors. If you have a high enough relation with both parties, you can help negotiate a truce. Or, if you have sufficient forces that you intimidate one of the nations, you might get them to back off.
2) Allow "Armistice" as a war settlement offer. Allows for the temporary cessation of hostilities, say, 1-12 months, without requiring a full five-year White Peace.
3) Fix the escalating costs of refineries, universities, etc. Why in the world should it be increasingly expensive to establish facilities?
4) Create local militias that would serve to defend home provinces, but they would not want to leave their homelands to fight foreign wars. If you take them outside your borders, they'd suffer huge attrition. That way you could really play a "defensive" (militia-heavy) or "offensive" (standing-army-heavy) game.
5) Allow creation of administrative regions. One huge sprawling empire should become inefficient to manage from a single global capital. There should be a way to create smaller subdivisions of a large sprawling state which would be necessary to manage a large empire. You might need to pay to build regional capitals, but it would help with stability, and so on.
6) Overhaul Reputation. If you are a large global empire, why is your annexation of parts of China alarming people in Bavaria? Shouldn't there be "reputation" towards Christian nations, "reputation" towards Muslim nations, etc., i.e., based on religion, or couldn't there be "regional" reputation, so that you might be seen as a hero in Europe, and a villain in Africa? Doesn't this actually reflect more of the truth, when a nation might have different pluses and minuses depending on the demographic audiences you're talking about?
7) Allow for cultural and religious mixes of provinces. Places rarely tend to go from 100% Catholic to 100% Protestant, even after years (or decades or centuries) of proselytizing. Similarly, there are often cultural minorities amongst populations. Allow for this by letting each province keep track of the percentage of minorities. There can be "splashing" from nearby provinces, modeling the migration of ideas and peoples over time. Narrowminded cultures would have less mingling, etc.
8) Control large empires more by "management span" rather than by "reputation." Right now, the thing that keeps the world empires from expanding is their concern for their "reputation" more than anything else. They have large enough armies to crush any uprisings. Those do sometimes succeed. But really what should limit their global growth is their ability to administrate large spans of territory, especially as it could take years for word to travel from one end of their empire to another. That's why I am suggesting the concept of regional administration. To put more focus on how to create centralized or decentralized states, and how to rule a global empire, rather than just stopping your conquests because you are afraid that Luxemburg might think you're a bully.
9) Allow for more than 3 advisors based on an investment in your Ministry.
10) Allow the hiring/appointment of foreign ambassadors.
11) Make the province decisions less idiotic so people might actually implement them more often.
12) Fix the "build" tab; don't show me that I can build refineries in more than 3 provinces, if you can't also show me the provinces where I can build them, and where I can build them for the 2x bonus.