Well it's been a few days so I figure I may as well post my thoughts about this game.
First off, this is one I've been watching for a couple of years now. I was disappointed when it was pushed back from last year to this but if it helped polish the game then it was something I couldn't really complain about.
Prototype is a very good game. It's verging on "excellent" (although that will depend upon how the story pans out) but has a few niggling issues which, on the whole, aren't enough to detract from the overall experience.
The graphics are good, although a little bland in some areas. The protagonist, Alex Mercer, is animated extremely well, though. He flips, jumps, grabs on to walls and glides perfectly. I don't know if he was motion-captured but it looks like he was because to me his movement is completely fluid and natural.
The story and writing is also a cut above the rest. Typically plot is a throwaway word in sandbox games like this and although Prototype moves in to the often-done government conspiracy territory for the story, the so-called "Web of Intrigue" ties it together in a very original and unusual way. Basically, you begin the game not knowing much more than your own name. You know that people are chasing you and that you have been changed; that's about it.
During gameplay you will see every once in a while a red marker on the minimap indicating that you are close to a WoI target. If you find and "consume" this person (which also gives you health) you will then gain access to a fragment of their memories, usually in the form of a ~20 second cutscene, which helps to fill in the blanks. There are over 100 of these people to find and several strands of the main story into which they fit. It's an excellent target-driven system that makes you watch the map almost all the time since these targets can pop up in side-missions, in main missions or simply while you are running around. Props to Radical on this, it's one of the best aspects of the game and is done very well.
As for the combat, Alex initially has only a few attacks available but even on those the animation is very well done. As you progress you will unlock more powers to use, such as claws for your hands (enabling you to easily live out your Wolverine fan-fic in-game since all your friends keep making fun of you when you try to RP it with them), hammers for your hands enabling large shockwave aoe attacks to knock down large groups, and also a very cool bola/grappling hook for an arm which lets you take out enemies and helicopters from long range.
Because I'm doing all of the side-quests too I am only 1/3 of the way through the game so far (there are 31 main story missions). It took me a couple of weeks to finish the last good game that I would put into this category, namely BioShock, and in the end I was meting out my BioShock playtime simply because I didn't want it to be over. I'm going the same way with Prototype, although it's easier as since it's a sandbox game I just stop doing the main story and go on a rampage somewhere or do some of the side quests instead without needing to progress the main story.
Speaking of the side-quests/minigames, they can vary from being a simple tracking mission where you need to consume certain people spread across the map within a time limit; a more simplistic obstacle course where you need to hit the marked areas in sequence within the time allowed; combat areas where you need to kill X amounts of enemies within the time and are only allowed to use a pre-selected power; and others besides. They are varied enough (although I suspect by the end of the game you will be wanting a little more diversity), and doing them well rewards you with Evolution Points which you can use to fund the purchase of new powers and abilities.
As for the negatives...on the PC version there are some technical issues, such as Radical deciding that certain resolutions require certain amounts of video RAM, even for quite moderate resolutions. You can read further details about this here, and it seems a somewhat arbitrary way of doing things that has won Radical no favours.
On the same link you can see details for a somewhat larger problem, namely slowdowns in and around cutscenes even on quite beefy PCs. For now a workaround is to go into your Device Manager and disable as many Human Interface Devices as you can, this apparently improves performance substantially and is a bug that should have been caught in QA but wasn't. Hopefully a patch for the PC version will be forthcoming, as I have personally experienced this issue quite extensively even on a very good PC. Most of the time I'm running at 50-60 FPS on 1920x1200 4X AA and everything on high, but every once in a while (particularly around cutscenes, as noted) the FPS will drop to under 10 making the game virtually unplayable. A workaround of my own that I have found is to drop to the ground level and run around a bit and the FPS usually jumps back up to the regular level within a few seconds and then I can continue with my gameplay as normal.
Activision are aware of the issues and will hopefully push a patch out very soon to address them.
I've already mentioned the bland graphics in some areas. Buildings aren't very detailed, at least in the beginning of the game, and some of the pedestrian NPCs also look like they are in a game that came out 2 years ago. These are minor quibbles though, and really don't detract from the overall experience very much at all.
The game also eases you in very gently in the beginning and then suddenly ramps up the difficulty as y0u get further in. The first 10 missions or so are not challenging at all and mostly serve to introduce you to the game, to show you the ins and outs of combat, shapeshifting, jacking vehicles and all that buttery goodness. Then from nowhere, I won't detail it here to avoid any spoilers, you get a mission that ramps-up the difficultly about 500 times, to where you (or at least, me) are constantly failing and what's worse, I couldn't even see how it could be done. Eventually on about the 12th attempt I completely fluked it, but from other reviews I've read the game does get very, very difficult to complete later on.
Vast open world
Powers are varied and effective
Some technical issues
Minigames/side-quests may get repetitive
Uninspired visuals in some areas
I'm not comfortable assigning a score to a game that I haven't finished yet, but if held at gunpoint by a crazed Infamous fan I'd say this game merits at least an 8/10 thus far. I'll post a final update on this once I have completed the game. Needless to say, Prototype is an excellent game that delivers upon much that Radical have been promising for the past few years of its development.