I think Prototype does it better, whereas inFamous forces you to be good or evil, as you play through Prototypes story you see this moral ambiguity. I mean, your character is kindof a hero, but then again he's also very much a sociopathic crazy in his own right.
The gameplay in Prototype is very satisfying, its like a combination of Saints Row, Hulk Ultimate Destruction, Spiderman 2, and God of War. The parkour is INSANELY satisfying, body surfing, gliding from rooftop to rooftop, running up the side of a building, its all so satisfying. With that being said though, inFamous was the first, and is still the only PS3 exclusive that has appealed to be. I'll be honest though, Prototype will sell better, its multi-platform against a console exclusive.
I'll close with this, its apples and oranges, Prototype isn't really you're traditional hero game, whereas inFamous is. They've both got good reviews, and i'm sure inFamous is a good game, and I know Prototype is a good game. My opinion is? If you have a PS3, get both. If you don't have a PS3, you still owe it to yourself to play Prototype.