Great movie, great score!

In the Matrix, once you are told that world Neo knows is a simulation, you accept that and it merely becomes background for the main story which is about Neo coming to accept what he is because he knows it, not because his senses tell him. In other words, he has to find faith in himself.

In Dark City, I never stopped questioning whether this was real or not. In fact, the city is actually a character in the film. In my view, it is not a simulation of reality, but a simulation of a fantasy. It seems clearly styled around film noir classics and presents a gothic view of world that never really existed. But the key difference is that it has physical reality, just a very bizarre one.

In addition, memory is handled very differently. In Matrix the memories are real and reality is false. They are just memories of things provided by the simulation. In Dark City the memories are all implanted by The Strangers. There is a real place and the memories are false.