No matter which ending you get,poor Aya loses in some way. Either she is simply killed, or made into one of her father's nightmarish creations, or manages to escape...only for it to be hinted that she's ended up just like her mad father. And the last one is the closest the player has to a 'good' ending!
By the end (the good one, anyway), Aya has lost both her parents and found out that one was completely insane and killed the other. Is it any wonder she decides to pick up where her father left off?
Coron. Poor Coron. All she wanted was to be a part of Aya's family. Made even worse when she's killed for trying to help Aya.
Maria getting attacked by the doctor in the Good End and one of the Bad Ends. After years of dedicating her life to the doctor, how is she repaid? She gets attacked and is left for dead. Depending on what you do, you can either save her or you can leave her to die from blood loss.
Aya's mother's real death. In her last moments, she called out her homicidal husband for wanting to turn their daughter into a doll. As a result, she planned to take her away and spare her horrific fate. Her husband retaliated by stabbing her in the chest and hiding her body in his lab.