I like this game, but is a mess structurally. Is there a best way or order to do the quests and activities and not miss anything? Like when should I start the Angels and Demons quest, before or after the bathroom scene, for example. Which way it makes more sense narratively?
Quests aren't exclusive, so you'll never miss anything unless you want to (like choosing to exorcize Ava/Lilith).
At most, some quests won't advance until you advance others.
If a quest is stuck (for example, Sacred Sex quest saying you should wait a few days, or talk to the priest) they're usually unlocked by either going to sleep in your room at night or by advancing other quests.
Quests don't usually have cross content either and when they do it's in the form of repeatable scenes (like the teachers from the alien quest and your cousin from the ghost quest).
The few that might less sense if you didn't advance another one are already gated behind that other quest requirement (although you never see that requirement, you keep getting the same hint).
So long story short, just do whatever you feel like doing. You'll eventually be able to finish them all anyway and you won't miss out on content (other than via choices, as mentioned).
EDIT:
Just rememebered that there is one thing you can miss out on. When you finish viewing the webcams from your aunt's house, during the sacred sex quest, there are 2 things you might miss on.
The first is that there are scenes in her house with all 3. If you keep advancing the quest they will be replaced with others, but you won't see those specific ones again.
The second is that there is another dream or two besides the ones related to this quest. At some point they stopped being possible to show (one even unlocks a card) if you advanced this quest. I don't know if the dev changed it since.
For this quest only, it's better if you wait until you get all dreams and until you've seen all scenes at their place.
Everything else is as I said, and nothing is missable.