* Shattered world is gone but there's two separate "Randomise Religions" and "Randomise Rulers" game rules that can do something similar.
* Ruler Editor is gone so no custom ruler starts (Paradox have said it'll be in a post-launch free update)
* Societies are gone but the secrets system has some elements of it (You can be a Witch, and can turn your house into a secret Witch's Coven for example).
* Charlemagne start is gone so the earliest start is now the Viking Era.
* The Treasury is gone, so only have the 'Pet Cat' attribute and stuff again.
* Nomads are gone.
* Cannot interact with China
Think that's all the major things missing from fully DLC'd CK2.
But all-in-all most of those features were never...thaaat great in CK2 by themselves, let's be honest. So they cut the things that didn't really 'work' and added lots of new features and streamlining around the idea of you playing a 'character' not a 'country' (The stress systems means suddenly obvious nope choices become 'maybes', for example). Character tree is a little 'gamey-feeling', but all-in-all it's a net positive I'd say. Ruler Editor is the only thing I actively miss, but could always just cheat to modify your character if you really wanted to anyway.
And in terms of potential modding, which let's face it is what all Paradox games become a sandbox for eventually, they've made a lot of things in the engine that were previously hard-coded data-driven so should be room for some pretty awesome Total Conversions in the future. They gave a few modding teams early access, so already have the 1.0s for a Bronze Age TC and a Vampire TC in the workshop.