Don't believe the hype.
Don't get me wrong, Prototype is fun at first. If you like overpowered god characters that run around bashing and slicing everything. The pain you can cause is only limited by your imagination. That's a good thing, for about an hour. Then the games shallow nature will surface itself after that. There were many moments where i was like "wtf is the point of this". It has a lot of cool ideas that if properly fleshed out could truly make a great game, its just the execution was done poorly. I can assume when the brain-storming session went during development a lot of people had cool ideas and nobody mentioned the word "balancing".
And it shows. As far as open world games go (this should be its own genre by now) its one of the better ones. Granted I had more fun playing red faction guerrilla and infamous on my PS3 (i've been weening myself off the xbox360).
Speaking on bad comic book writing, it can be done right. Check out Infamous if you want to see the correct way of doing a game like this. Prototype and Infamous can be compared since they both are essentially the same thing, its just that infamous has balancing and Cole isn't some unstoppable shapeshifing death machine.
You earn evolution points which you can cash in by pressing the start button and accessing the map interface where you can buy upgrades (moves healths ect). You'd think this would be a system that would slow you down but you can pretty much earn most of your moves very early on in the game since you get a crap ton of Evolution points. There's a stealth system somewhere buried in there that screams "novel idea" and would serve to make this title unique, but there's no use for it. The game has a disguise system that allows Alex Mercer (the hero or villain if you really think about it) to assume other peoples shapes by consuming them. So basically your a mass murderer. If they got the licensing from Marvel and just called this game Carnage (villain in the spiderman series) it would've done more thematic justice to this game.
The story takes from the standpoint of flash backs that happen in 3 day intervals over the course of 18 days as the days progress (they don't really progress the game cuts and jumps you to certain days as you complete main story missions). Lame. As its an open world game there are time trial minigames and races ect...which Totally ruin the feel of the game. There are blue orbs to collect for the obsessive compulsive crowd of gamers and there are characters that you can consume that furthers the web of intrigue system, this is basically a story mechanic, consume a soldier get a cut scene...since after consuming soldiers mercer now "knows what they knows". You'd think after he consumed thousands of innocent civilians he'd learn to drive or fly a helicopter and leave manhattan...anyway.
I can go on and on about the flaws of this game but that would take all day literally, don't be fooled by the user hype. Go back to my first sentence. This game is mindless and shallow and at best worth a rental.