Prototype was fun at first, but the meh storyline, sometimes complex controls and the spike in difficulty put me off quite a bit. It does have more free roam fun though thanks to the better powers.
Ultimately, however, I like Infamous a lot better. The story actually drew me in, the gameplay was fluid and fun all the time, and at the end I was literally like "Dude, holy shit!". The only bad part I found was sometimes the difficulty was annoying due to enemies perfect aim. I hope that is fixed somehow in 2.