I've played both games now, and before, I would've just said Prototype wins. But there's allot more to it than that. They both have their pros and cons but all-in-all, are both pretty good games. Amlost the same as a whole. Let me tell you why:
STORYLINES: Most people say Infamous has a better storyline, but after playing both, I may have to agree a little. Not completely. Infamous' story is told in a very direct manner, while still maintaining the guise of complexity. It let's the story unfold somewhat smoothly as you play, and makes you want to know what happens in the next cutscene. I must say; the writer is a fantastic one. Prototype however, does not (on it's exterior) seem to have much of an interesting storyline at all. The connection you should be having with the character isn't quite there, and events just seem to be unfolding with no propper introduction to them. Prototype's storyline is actually pretty complex and interesting once you've unlocked all the web of intrigue clips. I've come to find that Prototype actually has a more complex and interesting storyline, but it's so unfortunate, how they make you have to unlock all these web of intrigue clips to really appreciate it. I had to play prototype at least twice, to get what was going on. So Prototype's storyline is actually (as a whole) better than Infamous', but because it is not direct, I give it to Infamous!
CHARACTER GAMEPLAY: Cole (Infamous) is a free-runner with the power of electricity. He has quite a few abilities but lacks SPEED. I like how he free-runs his way around, but it can be quite a tedious form of getting around. At least he has power lines and railway tracks at his disposal (for quick sliding of one place to another) though. I like how you can re-charge his electric power off of anything conductive, but his attack abilities are too limited for me. While Alex Mercer (Prototype) is a Virus morphed into the form of a human being who's memories he is trying to re-attain. He has a maltitude of fighting abilities with devastating amounts of power, and is able to travel REALLY fast. His running is quite amazing, and he can go anywhere. He jumps to heights (that Cole would take a few mins to CLIMB to) in seconds. You can fly helicopters and drive tanks in Prototype, but can't drive/fly anything is Infamous. Alex Mercer clearly is the most powerful of the two as well. Comparing the two would be like taking spiderman (Cole) and putting him against a Hulk and Superman combination (Alex Mercer). So this one goes to Alex Mercer!
GRAPHICS: It goes to Infamous. Full stop! But Prototype is also quite the nice-looking game.
ENVIRONMENTS: Prototype's has it seperted into sections of destruction and sections of peace. While every aspect of Infamous' environment is destroyed. I didn't like that at all. They could've at least had a few normal and peacful areas. So Prototype gets it here!
LENGTH OF GAMES: They are equally long. Prototye would be a bit long because you have to spend time finding web of intrigue targets after you finish the game. And Infamous is a bit long because you have to play the game twice (once for good storyline, and once for evil storyline).
OVERALL: Well it just boils down to preference and fanboyishness. If I had to pick ONE game though, it would be prototype, because the character is just so powerful and fast. And the environments aren't all destroyed. But for the initial "Haha cool" that Infamous brings, Infamous gets quite some points. So it's neck-and-neck until the sequels release
