I have to disagree with the only using the extendo arm or mr.Fantastic appendage as I like to call it all the time, I while playing often tried to vary using each weapon, and while the extendo arm was useful to fight of some stronger mutants at first, it quickly became a weapon I only switched to for fighting helicopters and taking them, or for brief momments in combat, The muscle mass power was my favorite as it could be used with all the combat moves and was super powered (one kick to take down a helicopter) and all the others I used equally, except for the claws which was less. I never used the vision abilities really. But i did use guns, they could be pretty good, and the armored form was cool, but not being able to dodge roll made it suck against the super mutant things or super soldiers which would just keep hammering you down if you couldnt move, though avoidable, still could result in more health lost.
Now having played both games, prototype in my opinion wins because it was just more fun, the attacks didnt all have to be ranged, enemies were not always the same little group, and the military etc was at least doing something, and I wasnt tied down by moral choices, where I wouldn't shoot a grenade into the streets for fear of killing some civilians, only to be rewarded with a F-you at the end of the game where the evil side can basically get a super powerup, and a good guy cant. I agree the side missions made more sense, but prototypes also make sense as a distraction from just killing everything in story mode, and force you to use other powers to see the benefits etc...and guns were helpful.
When it comes down to it though, now I have 2 awesome games to play so am i complaining? do I care which is "better"...no, because they can appeal to different people, no one is just better. What prototype did for me was that it felt super, you felt almost unstoppable (though you could be killed if you weren't careful) for the whole game, even at the beggining where you had few powers. where as with infamous you feel kinda meh for a long time.