I bought this game a few days after release, I was really pumped. I traded it in yesterday for Resident Evil 5, after completing probably about 1/2 the game. I almost never sell games back, and never do it without beating them first, but this game lost me.
The "stealth" options were broken; I would jump off a building, snatch who I needed to impersonate and run away, come back 2 minutes later and walk right into an objective. The combat was interesting at first but seemed a little to 'twitchy' for me.
But my main gripe was with how extremely easy it was to navigate NYC. It should have been amazing fun to move around that city, but instead you could literally just hold forward and the run button, and never fail. For instance in the spiderman games you had to very carefully swing to keep your momentum and speed going. Prototype doesn't punish you for failing and falling down at all, you just hit a wall while falling at 60MPH and BINGO you are instantly, with no momentum loss, running up it. The city itself was also extremely bland, lacking detail.
The game world was interesting, with the mutants and such, but it just couldn't hold me. A big let down for me, I was pumped for this game.
Lately I find I play Gears of War 2 and Magic online more than anything, despite having 3-4 relatively new games sitting there unplayed. Consistent, quality games (though Magic is ridiculously buggy).