Well, I must be some kind of thicky because I actually enjoyed the story of Prototype. It was one of the few to use the cliche' of Amnesia (Fun Fact: Accidentally getting powers is cliche' too) well as in you had to actually deal with it as opposed to it being some side salad dressing to add depth.
The amnesia actually makes a lot of sense when you get through the game and discover what actually happened to Alex Mercer. I had a hard time taking his annoyance at the conspiracy part being something to figure out... Well, it's a conspiracy. You have to find the puzzle pieces or it isn't really a conspiracy, just exposition wanked in your face like a bad porno. I actually enjoyed finding out what all went down by finding all the Web of Intrigue targets.
As for craftsmanship, I've seen InFamous. I wasn't exactly impressed though to Cole's credit he is a two trick pony. He can pistol shoot lightning from his hands and toss electrical grenades. The morality kick wasn't that impressive, if anything, it seems like a lackluster way to force you to play the game twice as opposed to inviting you to do so.
To be fair, I am not knocking InFamous, the only real criticism I can find is that I didn't see a targeting system and that just annoys me.
InFamous is based on a guy who gets power through an accident and then has to be Good or Evil. That isn't a set personality, that is a case of schizophrenia. Again, not bad but I wouldn't call it set as the player can dick about so Cole never knows who is or wants. That is the beauty of faffing about with morality. The missions have a great variety because he has to make moral choices, which is to its credit but morality shouldn't be a main course here and never should be.
For those seeing my Prototype bias, I apologize. I am a hands on kind of psychopath so Prototype had me anxiously waiting with school girl-esgue preprom jitters since I caught the Game Informer article teasing me about it.
Prototype follows a man who discovers that he was dead and now a monster. Sure he is confused and questioning his actions as he does them. He doesn't know who or what he is, just that somebody needs to pay. I have to agree with a number of other people here, Whipfist was great but it wasn't the end all for me. You trace the lines along the Web of Intrigue to find out what is going on and who you are. Your body is agile and upgradable with health only a squishy human sippy box away. You can run around in tanks or helicopters and as Croshaw pointed out, there are a ton of ways to be a dick in a most cathartic way.
Sure the events and missions weren't excessively varied but I honestly am glad for that. You're a walking biohazard with the powers to maim and destroy life on a scale that makes me squee, which is not something I do often. Not much else to expect. You aren't there to faff about your morals, you are there to kick ass, kick some more ass, take a breather by being a jerk, then kick some more ass in creative fashions. The story had me interested and I found myself scouring the city for those Web of Intrigue targets in the post game and actually delighted that somebody used Amnesia as a game mechanic that helps the story instead of a BS flavor crystal on a wad of nasty gum.
/rabbling