I played all three to the end. I think if I could combine the option to be POE1 and 2 combined then I would give that best overall story - and story means to me how interesting and fun the story is as well as how it meshes with overall game play and role playing. A story that is disassociated from the game, which some can be in games, would get a low score from me even if a good story. The story has to be intimately tied into the game itself.
But just POE2, DDOS2, or PK then I would go with PK. There were lots of plot twists, lots of choices and consequences, lots of history and lore, and felt the story went very hand in hand with the game play and role playing your character.
I could care less if something is simple, complex, cliche, unique as long as its fun, engaging, and interesting to me. I liked all three stories in all three games a lot. But between the three PK edges out above them because I really enjoyed it.