So, after way too much time wasted on this game, here are (some) of my gripes with it, in no particular order.
1. Genetics game is way too easy. By year 1200 all of my children were guarantied beautiful herculean geniuses. And it wasn't just my children - this combination was very common in my entire dynasty as well. It got to the point where there are 200+ geniuses running around in the world, most of them also physical gods, and 99% of them are related to me in some way. My Übermensch blood has even started to spread into other kingdoms, when I see handsome genius king of Italy I know if I go back through his ancestors I'll run into someone from my dynasty, because the AI simply does not play this part of the game.
2. Making money is way to easy. By year 1200 I have an income of 200+ per month, 200k reserve and another 100k in my piggy-bank archbishop that I can break open at any moment. Now, that happened in CK2 as well, but the problems is, I have nothing at all to spend it on here. I've build every barony in my empire, fully upgraded my demesne, I hand out cash gifts like candy. Upgrading every building in the realm is just too tedious to contemplate, and there are no massive money sinks I could invest into.
3. AI is hopeless. I hold Britannia and coastline of France and have 120k of manpower. ERE holds most of Europe and Africa, is better developed than me and has 30k. How is that even possible? And how the hell is the Basileus so damn poor, what does he spend his cash on? Oh, and the Mongols are a joke. Got a warning about an unstoppable horde, I look it up, and they have 30k. So scary. 30 years later, Khan is dead, maybe they will stop their rampage now? I look it up again, they never even got close to Europe. Wow, such carnage.
5. The AI is also way, way too damn aggressive. Before I could raise my crown authority to put a stop to this, there was never, and I mean never a time without at least a couple of inter-vassal wars happening. Hideous internal borders, nobles killing each other in a giant free-for-all, countless armies running rampant all over my realm, everyone ganging up on any poor new guy I gave land to, it was awful. I had a smaller neighbor I shared my faith with - in a span of 50 years I had joined them at least 20 times to defend them against holy wars, before finally giving them up as hopeless. The AI sees someone with less men that they can declare for on - they do it, regardless of any other circumstance. Pope is another special (head)case here. Just how many times do I have to kick his crusading ass before he picks an easier target? The first time he at least had comparable numbers, but by now it's getting embarrassing - 15k vs 150k? I feel like I'm hitting a special needs kid.
6. The whole fervor mechanics should be thrown into trash. How the fuck does it make sense for winning over the infidel to make the faith weaker, and losing land and worshipers to make it stronger? Fortunately I made my religion pacifist to avoid this nonsense. No holy wars for my idiot vassals, no uppity vassals expanding their power base, or crashing down my fervor. Well, this way at least, don't get me started on that stupid sinful bishop event. Freaking 10%?! No wonder Catholicism is dying in every bloody game.
7. The AI is also fucking insane. God help you if you have sadistic assholes in your realm that decide to pick intrigue focus, because they can decide to start randomly murdering people. Like your heirs. I lost more than a couple heirs to this, and it's always the same story. I get a warning from my 30 intrigue spymaster that someone is plotting against my heir, 95% chance of success. Well, that's just great. The heir does not have any rivals, and neither do I. Nobody has claims on his or my stuff. It's not the spymaster, he's firmly in my pocket. People next in line for the throne are content and love both me and my heir. Hell, everybody likes us because of our traits and the way I set up our religion. Finally I use console to track down the bastard doing it, and it's always some random nobody asshole vassal with no possible motive whatsoever. And because in a large realm there are always at least a couple such high intrigue assholes around, both as vassals and as guests you can't stop coming to your court, there are always more than enough people around to join their inane plots.
There's probably more, but these are the things that came to my mind first.