It's not that the story was complicated, it's that it was just ... bad. Lazy. Boring. Had all the depth of a muddy puddle.
Runners are good because they said so. The corporation is bad because they said so. I dunno, but the city seemed clean and fairly well maintained. It really didn't seem that bad, and without expanding on why the runners exist you just get the impression that they're crooks fighting cops because because because.
That being said, the gameplay was still pretty fun. And the DLC is a step in the right direction. Nuts to story elements, let's just give them a play ground to run around in. Good!