Infamous has a much better story and characters than prototype i also liked the visuals more, the side missions are varied enough to keep them fun and they have an effect on the game. Main issues were issues with the speed that you can move around in some areas and the small scale combat.
Prototype large scale insane combat, being able to replay with all your powers from the time before, vehicles, the entire game map is unlocked from the get go (wish more sandbox games did this). Issues drab city in terms of color and variety its rather boring, character not as interesting, story left a lot of unresolved issues, like what happened Alex's sister, after one mission she just vanishes.
I liked both games and still play both every once in a while.