I don't know how difficult this would be to implement, but I feel like some of the events/quests need to be able to influence certain parts of other ones. For example, after Rahi tells you about how she ended up at the prison, your should be able to tell her exactly what the drug used on her was if you've done Tavi's quests, especially if you allowed Tavi to test the drug on you. Another example is when Nova appears during one of Tavi's quests. She shouldn't be introduced as if it's your first time seeing her if you've interacted with her before.