I don't have a PS3, so I only played Prototype. But even so, I think that Infamous might be better than Prototype if only for the story. Prototype had a plot that managed to be simultaneously complex and boring. I've lost count of how many times I was 1 inch away from a web target and then because I accidentally bumped into him with a shield, he died. And the army have this wonderful habit of killing your target. And then you have to wait for a few minutes. And then he dies again.
What fun,eh?