Maybe Larian's universes do not come with such things as "mental" attributes to begin with, and maybe you are just mistaking what they are doing for a D&D clone. Dragon dreams, spirit world? I'm not that sure such things are relevant to the Divinity lore, but if you want to mod them... Well, just use your imagination to force the player into resting. Maybe mod a rest system and cleverly weave it in the vanilla gameplay.
Crafting is present, but I agree it needs more love. As in, more explanations, more info on how your skill will improve items. World interaction systems, I'm not sure I'm getting you. Respawnable areas, no-no, that's not a standard " rpg point " as it entirely depends on one's conception of rpgs and there is already a whole thread dedicated to the debate on handplaced and finite enemies vs respawn. I could also agree with the fact that quests are "only" giving you XP, BUT here again it's personnal opinions. It's also ignoring the fact dialogues and specifically arguments are improving stats based on how you chose to resolve them.
I think your issue is that you're mistaking D:OS for ... something else. An Elder Scrolls game, perhaps ( which I'm okay with, I love them ). But in truth, I don't even really get your point, as I don't see how your examples pertain to the "freedom" you speak so much of.
To be honest, I'm not even sure pure freedom is a good thing in a video game anyway. It's probably okay when you're playing pen and paper with skilled players ( I saw some open-worlded P&P games, if I may say so, fail because the players had no idea what to do and deliberately chose not to follow the plot despite the GM's best efforts to set them on the right path ).
And while I didn't play Divine Divinity, Divinity 2 was a very straightforward game, which wan't preventing it from being a fun, clever, and ultimately very good game.