Or Nier, which are inspired by and connected to Shadow of the Colossus in the same way as SotC is connected to Zelda (explicitly mentioned in the article)
Agreed, Nier: Replicant definitely belongs in the list. Yoko Taro successfully asks "What if the opponents you fight were the main character of their own stories with their own good and justifiable motivations?" as well as any of the other games mentioned.
Came here to mention the same thing. It's one of the pillars of the whole Witcher saga, but most clearly it's visible in Sapkowski's short stories - The Lesser Evil, A Grain of Truth, A Question of Price, The Witcher, to name just a few.