1) Satanic society, semi-fantasy half of hermetic society, immortality, religious rituals actually giving material benefits magically out of thin air etc. Supernatural stuff in general. It also tends to break balance by its very nature. Yes I know we can disable it in ck2 but I prefer if devs didn't waste any time for its at all.
2) Too much priority for very niche, dead, undead or borderline fantasy religions, instead of prioritizing major religions. With all due respect, Islam, Orthodoxy, Hinduism and Buddhism (if you wanna include India) should get WAY more attention, polish and flavor WAY before we get into nitpicky borderline fantasy stuff. I do enjoy Holy Fury pagan mechanics but it's ridiculous pagan faiths got way more attention that freakin ISLAM, probably more central religion to this time period than Christianity (certainly more advanced before 12th century).
Polish main religions on release, balance them in patches and only then pay much attention to Slavic paganism, Manichaeism, Zoroastrianism, Judaism, Taoism, Bon and whatever dying or geopolitically marginal rate religion (assuming 867 start date).
3) Strange systems of Jade Dragon, either straight add China or don't bother with spending half a year of dev time and resources on weird box interactions players won't use 95% of time.
4) 769 start date. Impossible to properly balance and leads to crazy results warping medieval world way too much.
5) Tactics system. It is simply incredibly overcomplicated. You either don't look into it and compose troops basing on blind intuition or need to memorize like 300 different numbers from wiki.
6) Defensive pacts, nothing like AI Mongol invasion because everything between Egypt, Pakistan and Finland is in three insane 20th century style rock-solid power blocs. Idiotic solution both from gameplay and historical perspectives.