On my opinion the main flaw of the game is the very poor combat system. I have played about 1k hours to EU IV and V2 and I hate it when I have to go to war. Every time, war consist in basically, moving your army to an enemy province, wait until it is controlled, then move to another province and so on. It takes hours, it is boring, and annoying. Controlling an enemy province is just automatic, it only takes time (and some casualties to attrition). EU II had a better system where you could choose to siege, assault (which means a battle with defenders that you can loose) or surround the province.
I think that the main problem for the AI is that for a given war, there are no strategic points, victory points or objectives that will make you win the war ( these should be related to the Casus Belli) So, the AI just doesn't know what to do. Give the AI clear objectives and victory points (like key provinces or fortresses in the war) and will be much better. Since there are no objectives, or any tactical possibilities to use, any war implies armies moving around the map taking provinces, which is absurd. If I declare war against France to take Martinica, why are the French sending their army to take my colonies in north Africa? Absurd. Then you are advancing to take the enemy capital, and the AI doesn't care, they prefer to use their army to take one of my provinces with no value for the war.
This stupid combat system it what creates so many issues with the game, because to compensate for that, many other stupid and annoying rules and mechanics must be created in order to avoid that big countries just go around eating smaller countries too easily. And I think that is the problem. Instead of fixing the original problem, they add more stupid mechanics to compensate.