I actually regret buying Prototype. For one, it was quite expensive back in the days (somewhere around $80). The bigger disappointment was the gameplay; it was horrid and repetitive. If you didn't do the side quests, you wouldn't have enough points to upgrade. On the contrary, if you did, you'd be bored out of your mind (like I was) before you reach the middle of the game. I stopped playing after the first Supreme Hunter encounter. Each boss fight was basically: run around and use your tentacle hand. The gameplay could have been remedied with a better character, plot or challenging enemies (super soldiers) that didn't just appear once every blue moon. Sure, I've heard people praise the Elizabeth Greene boss fight, but no one buys the game for just one boss fight; unless you get to fight Hitler whilst attempting to rescue an entire encampment of Jewish prisoners. Even then, $80 would probably be a huge disincentive.
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SPOILER
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By the way, why is the game even titled "[PROTOTYPE]"? Mercer, as far as I know, was the result of an accident related to the virus and is not the archetype of the virus as it was released elsewhere prior to the game's plot.