These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
In Prototype2, the Penny Arcade comic showing Mercer karate-kicking a helicopter is used as the decal for an achievement involving karate-kicking a helicopter.
Catharsis Factor: For one thing, after picking up a human-class entity, the only usual options are to either hurl them or eat them.
The statistics page in the game tells you roughly how much you've vented to date.
Complete Monster: The Real Alex Mercer. Not only does he brag about making a deadly virus 10x deadlier, when asked how he felt about his work and the human test subjects involved, he replied, "I wasn't being paid to feel". Even worse, when he was cornered by Blackwatch agents at Penn Station, he decided to unleash the Blacklight Virus on Manhattan, resulting in the deaths of over 10 million people in a truly callous act of Taking You with Me, even though he knew his own sister was in the city at the time. The man-eating virus itself even expresses disgust at what Alex did.
Crazy Awesome: Almost everything you can do in this game. Kick a helicopter to death, throw a car at it, throw another helicopter you just shot down at it, throw people at it... the possibilities are endless.
Which is all the more ironic that the Devs went the Friendly Rival route.
Foe Yay: There's a disturbing amount of this between Mercer and Greene. The Supreme Hunter is effectively created in a metaphorical birthing scene after a metaphorical sexual moment between Mercer and Greene. And given the protagonist's true nature, it could probably be seen as Parental Incest as well.
Game Breaker: The Air Slash move using the Blade. On every difficulty but Hard, it can one-shot Hunters, Supersoldiers, any kind of tank, and helicopters if you can manage to get above them. Leader Hunters go down in two. Double those figures on Hard. It tracks almost perfectly over significant distances, too. The only down side is the recovery time, which is small but noticeable.
And the charge-up time gives your enemies plenty of time to shoot missiles or tank rounds at you, interrupting the attack and sending you to the ground. As long as you have a clear shot it's a Game Breaker; the more heavy weapons fire you're taking, the more it leans towards Awesome, but Impractical.
Any blade attack in general does significant damage. A couple of normal attacks with the blade will blow up tanks, without needing the charge up time for maximum effectiveness of any of the special attacks. Put on your armor and whip out your blade and you can slice your way through anything.
First, those damn virus detectors. Their high-pitched whine and very short sabotage period render them almost too much of a hassle to deal with, and they'll be in every army base a few missions after you learn they exist. Worse yet, they get more numerous as you progress, making it near-impossible to shut them all down without getting caught. UAV versions show up, too, which can detect you almost twice as fast and follow you even if you leave scanning range.
Next is the helicopter Strike Teams, which are completely relentless. As you get stronger, they come in larger groups, and they eventually come with UAVs to detect you if you try to go sneaky. There can potentially be as many as four helicopters escorting five UAVs in the late-game. Even though they have to be called in by the military, the officers will do this within thirty seconds to a minute after you start a fight, and the window to kill the guy calling in the Strike Team is only a few seconds. What's worse, said guy can potentially be a tank. Thankfully, they're not terribly hard to kill, and it's even easier when you can skyjack the strike helicopters.
Third, there's the mid-level Infected civilians you usually fight during missions and events. Normally they're not so bad, just being about twice as tough as a regular Infected civilian and very fast. However, play during one of the events where you have to use a grenade launcher, and they are frustrating. They run around like they're on a permanent sugar high and will constantly run right in front of you just as you fire your weapon, resulting in you blasting yourself onto your back over and over.
In New Game+ mode, it doesn't matter where you are - there are a couple of tanks on blow-up-Infected duty right around the corner and they always decide to turn down the street you're on. "Look dude, I was doing just fine cleaning up the Infected on this street all by myself. Why don't you try Lexington Avenue; I hear they're pretty thick over there."
Even when you have several powers that can slice through Hunters like butter, they'll continue to be a nuisance throughout the game simply for the fact they can chase you anywhere and can obnoxiously combo you up close if you let them. This annoyance is amplified during the boss fight against Elizabeth Greene, since three at a time will keep spawning and chasing you while you deal with One-Hit Kill shockwaves, thrown debris, homing attacks and having to run away to consume things for health constantly.
Guide Dang It: The Web of Intrigue. Only about half the targets you need to consume will be easy to find, and you'll likely find them by accident or by consuming military targets. The rest only spawn in certain areas (even if the Infected have taken said areas over), and only if you've consumed the previous ones in the chain. As you fill out the Web, tracking them down becomes even harder. Worse still, they can be killed, and won't respawn for several minutes. You also have to be pretty close to ground level to get them to spawn in the first place, so a flyover with a helicopter will only work if you practically skim the pavement.
Harsher in Hindsight: "My name is Alex Mercer. I'm the reason for all this. They call me a killer, a monster, a terrorist... I'm all of these things." Come Prototype 2, and Alex, aka The Blacklight Virus is indeed responsible for the new viral outbreak and he is, indeed, all of those things.
Moral Event Horizon: Alex Mercer, both for his work in making the Blacklight virus, which was nasty enough before he got there, TEN TIMES as lethal as before. Also for unleashing it when cornered by Black Watch after he stole a sample.The player themselves can gleefully slaughter anyone they please, though civilians don't net you any EP unless they're infected. As well as Blackwatch infecting Hope, Idaho for no better reason than to test out the virus on people.Even the virus itself is disgusted by the actions of Alex Mercer and the higher-ups of Blackwatch.
Player Punch: Congratulations! You're The Virus! As an added bonus, even though you're a deadly virus specifically designed to kill people on a massive scale, you're a better person than the original Alex Mercer!
That One Boss: The second battle with the Supreme Hunter, aboard the Reagan. It wouldn't be so bad (big guy throws out an attack you can dodge, then hit him while he's recovering), except he's constantly getting shot at by aircraft, helicopters, and rocket-toting soldiers. This does next to nothing to him. But if you try to attack while a missile hits, you'll get knocked back and a decent chunk of health is knocked off. Depending on your luck, it ranges from frustrating to inducing the paranoia that the boss and military are working together to piss you off. The time limit doesn't help either.
In hard mode, the fight gets even more annoying because That One Boss is constantly blocking many charged attacks and happily uses new abilities copied off you such as the ground spikes. Throwing stuff still works, though.
Hard difficulty makes every boss That One Boss. Even Cross, the very first boss, becomes a nightmare to fight, if only because the delay between firing and going into counter-mode is vastly shortened, his grenades have a much larger explosion radius, and he both reloads and fires a whole lot faster.
That One Level: The three levels where you're infected with the parasite. Imagine the level where you first meet the Hunters times three. The only thing good about the parasite section is that its end gives you slick armor and the blade.
That One Sidequest: Getting Platinum medals. For instance, on the "Raid" War Event, which requires a time of 1:25:00. For every other event, getting Platinum is mostly a matter of skill (or cheating). Not here. You have to use a grenade launcher, so no powers, and there's 18 Hunters out of 36 enemies kill. Moreover, the spawns are woefully screwed up. The game will sometimes withhold new targets for as long as 15 seconds, and just to spite you, it will do this on the very last enemy. If that weren't bad enough, it is impossible to succeed on your own. You have to count on a tank spawning to help. Just like the enemy spawns, it is completely unreliable, and you'll be lucky if this thing even shows up until halfway through. Assuming it does, you have to hope Hunters are the only thing on-screen for it to shoot, that it doesn't get bogged down in traffic, and that the Hunters don't gank it on sight before you can get their attention. It's a Luck-Based Mission.
"Kill: Street Sweeper" is just as luck based, but also requires much more precise positioning of Alex, lest you not get the kills needed.
All of the movement events except for Free Running and Corners (if you know the trick; Double air dash in the streets while heading to the 2nd last and last checkpoints). Precise movement is required, with an analog stick at that. In most cases, one small mistake will cost you, and there are plenty of opportunities for a mistake. The worst two offenders are Eaves Jumping and Rooftop Runner. In the former, it's mostly a simple path, except you must run and airdash along narrow rooftop, and moving Alex to the side for a moment, even while not airdashing can cost you. The latter requires several sharp turns, with the camera being not too cooperative in helping you aim as you turn.
"Kill: Irony", not because it's difficult to get the points (you can cheat by blowing up a line of hijacked tanks for free points), but because the weak APC is likely to get brought down by RPG-toting soldiers before you can complete the mission and actually get credit for it.
What Do You Mean, It's Not Symbolic??: The level in which you fight the Supreme Hunter while a nuke is counting down is called One Thousand Suns, a reference to Robert Oppenheimer, who was himself referencing (or at least thinking of) the Bhagavad Gita, Hindu scripture, after the first successful test of the atomic bomb at the Trinity site (during what was, for extra fun, called the Manhattan Project). In three words, the developers crammed references to world-destroying superweapons, scientific progress and consequences, the phrase "I am become Death, the shatterer of worlds," a religious quote, and two puns. ...Or maybe they were just talking about the nuke. It's hard to tell.