Gordon Freeman wins. Yes, he wasn't included in the Prototype vs InFamous contest but he would win.
anyways, I think Yatzee is right about the winner. not in the way of going about it though. Alex does more then shoot lightning until a weak spot opens up and then shot more lightning. He makes pointy objects and then impales and eats them. And Jackie can make dark tentacles, summon darklings and use a bunch of different kinds of weapons... Back to the point. Alex doesn't chose to be good or bad, he's evil and always turning the streets of NY red. Cole can be evil or sissy and if you chose good, he's all nice and won't hurt anyone to much it seems like because ALL good (as in nice) super heroes are like that, meaning Gordon Freeman wins... or Jackie... or NEVEC... or Kirby (that little cheating bastard. First copy Alex, then kill both Alex and Cole.)