Aside from the overwhelming graphical problems and deficiencies, and the many bugs.
1. New Region system: Good idea, flawed execution. Too many provinces for one region. Very little info in the tooltip on how to properly manage(3/3 generals all full stack and cannot move out of garrison or revolt, even with the proper offsetting buildings and minimal squalor) how they work. The UI for the Region system is just awful and overly simple/dumbed down. Completely dumb how one province gets actual defenses. Overall it makes the map feel very small and conquests pointless in some situations.
2. General system + faction screen: WTF I have to have a general to have an army, yet you cant decide how many generals you can have, and you have a limited selection(family/tribe etc.) to choose from leading to balance problems with the faction under your rule. Merging units has become a complete hassle. No family tree in your faction screen, but you can just marry randomly for the cheap price of 10,000+..
3. The CAI/BAI/diplomacy atm is garbage: I really dont play a base TW game expecting the AI/diplomacy to be any good. I always rely on modders for that, but Rome2 has hit new lows in awful programming/testing. The CAI just does nothing 95% of the time. The other 5% they will put an army in defense mode or fleet in raid mode in my territory. Most of the game I'm wondering if the AI isnt glitched out/stuck or something. The agents are active, but thats about it. Even when I'm tearing thru their turf they just feel like maybe its a better option to take its stack and leave the city undefended as they go off in the other direction. The BAI doesn't attempt to do anything besides fight in a blob and get easily encircled as they all go to center mass. The fights are so buggy/so fast/so skill-less/so BORING. Diplomacy - nobody wants to do anything at all until you get 4 provinces and then you just basically bully everyone into trading or joining your confederation etc.
These are my experiences playing 2 factions 50-60 turns each on very hard. Rome2 is making some of the worst C&C games look godmode right now.