The biggest problems I've had are with the tank system, the AA/aircraft system, and the suppression system. The tank ap system is wonky when I see my Panther being shot by plinkers from a Stuart to the frontal armour, and the Panther crew bails/panics because of it. Also German optics are, for whatever reason, all rated as Bad to Very Bad, and they can't make hits in combat that would have been easy to make IRL (let's not forget the Germans noted a ~95% hit rate in combat on first shot at ranges around 1000 yards, and 100% at closer ranges). This makes tank combat awkward to me, with lots of slow aiming, slow firing, and long times to get even a single hit on a stationary target. This basically means German advantages in range/penetration/armour/optics are all moot when you can't even hit the allied tanks that are out in the open and simply bum rush your Pz4 or Panther (which, as FHer's, we all know was not the case in real life).
The AA system is wonky because AA seems incredibly weak and nigh-unable to shoot down a single enemy aircraft. AS we know here, AA was extremely deadly, the allies lost hundreds and hundreds of planes to AA during Normandy, and it was by far the main killer of enemy planes in WW2. Meanwhile the aircraft all seem far far too effective- I'm able to carpet bomb shit to death with a Ju88, pinpoint rocket attack enemies with a Typhoon, etc. Hell, even if I miss, the crew/infantry is so panicked that they're still pinned or retreated for what seems like ages past when the enemy is long gone.
This goes into my problem with the suppression system- the enemy can suppress your artillery with a few machine gun bursts, then comfortably ignore it for a long time or just walk up and take them out across open ground without hassle, because your guncrew/infantry is still cowering despite not being under fire. Same for retreating- an infantry man is not going to retreat through enemy fire- he's going to hunker down and panic, possibly surrender, or try to crawl away. The fact that you can't really select infantry formations (like dig in/prone was in Blitzkrieg) means that inevitably your infantry/support units get bogged down when they come under fire, and vice-versa with the enemy. While it's realistic to be able to force them to go to prone and have to slowly crawl under fire, they should still be able to shoot back and move around, albeit slowly. Hell, there isn't even hand to hand combat options, so you literally can't order a final assualt even if you do get close enough.
Basically, I see a lot of promise, but there is stuff I want to see modded to bits, or try modding myself. Thankfully, they are supporting modding.