My personal gripes about the game (some of them could be fixed in game files, but not all of them) are:
1) Lineup of buildings:
Buildings like Aqueducts or Granaries are quite nice and give a fantasy of growing the city, but some of other buildings are weird, especially the ones which changed ratios of pops.
2) Pops effects are a bit gamey:
My inner sense of justice tells me that everyone should pay taxes and manpower, so every pop should have at least these effects + something specific like trade routes/research for nobles and citizens (I think that both of them should have both but maybe with different focus). Interaction of slaves and produced goods (and goods/trade system themselves) is a culmination of the gameness.
3) AI:
I often play games as an observer and watching how Carthage was not able to kill sardinians in his own war until he decided to hire sardinian mercenaries was frustrating - armies are standing in africa, fleets are standing at ports, sardinians are looting their provinces, but naval landings are simply not happening. Another weird thing is alliances: AI could be much more proactive in its guarantees and alliances to create powerblocks against empires. Even if it has 10 diplomatic relations and people around agree to become allies, they often just don't do it. AI often negotiates weird peace which affects complaint 5.
4) Legions are removing cool elements introduced with levies:
Levies were a very cool idea, but after you pass legions laws, there is little reason not to use legions. And when you use only legions, the game turns into the same gsg thing but worse, because AI's usage of legions/levies is worse than AI's usage of the usual hirable armies. Levies introduced a very cool concept of not being able to concentrate all your forces wherever you need, so when war starts, you need to mobilize your local armies, influenced by the local population, and move them to the affected region and during this period, opponent can make significant gains or loot your provinces. And all this fantasy is lost the moment you activate legions laws. As a result, playing with disabled legions is more fun, but there are levy composition bug and some general problems with AI calculating the strength of levies. Changing something about this situation is important.
5)Rebellion system could have more work.
Low civil wars threshold improves the actual stability of the realm for the cost of killing 2 states wide rebellion when civil war loyalty modifier falls off. Provincial rebellions need some way to coordinate/choose time for a rebellion and not just rebel to die or get peaced out just before dying just because of some glitch in AI weights in peace negotiation.
6) Observer mode is lacking features from observer mode of eu4 and some stuff just doesn't work in it, like going to the country screen from pressing a flag in a province.
7) Characters.
Instead of random events with 10 pages of writing, I would personally prefer if characters played some very simple game of investments, trading and gathering popularity with proper interface to see the list of them, their locations, assets and their current actions. I think these events were a major part of the "characters are pointless and irritating" complaint: events about characters you have never seen with a wall of text which implies that he is someone influential are more irritating than interesting: you are not exposed to the narrative of Marcus building up his riches and influence before you see the event about Marcus's attempt to coup your leader.
8) Finished nomadic tribes.
9) Laws, national ideas, heritages.
Many of them are modifiers, like +5% citizen ratio, +20% import tax. It's hard for me to care about them as they are slightly more interesting than eu4 government reforms. I think they could be more fun if the amount of them was reduced, but the remaining ones were game changing, which could change the entire playstyle.
