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.
YMMV: Prototype 2
Anti-Climax Boss: Most bosses aren't difficult. Even the final boss is pretty easy, just so long as you don't use the exact same power he's using.
Broken Base: Since the earliest trailer the base was split between the people who were very upset at Alex being the villain and those who just wanted more Video Game Cruelty Potential. This continued on well past the game's release.
Creator Killer: The underperforming sales of this game were cited by Activision when they started layoffs at Radical Entertainment.
Crosses the Line Twice: Blackwatch is full of psychos, but Stanes, the guy who makes jokes about celebrity-lookalike infected 'celebrity headshots' and claims infected females look "pretty hot if you put a bag on their heads," goes all the way around the block and to pure comedy.
Game Breaker: Immunity to bullets and finishers. The former renders at least 75% of the military impotent, and the latter makes Armor and helicopters a joke. Once you have the shields, as long as you've got decent timing and pick off the rocket launcher troops first, the military is pretty much just walking snack food. Good timing with the shields also renders Orions, Brawlers, and Evolved pushovers as well.
Epileptic Tree: Many (if not all) fans have come up with multiple reasons as to why Alex became the Rogue Protagonist. Most have come up with ideas that suggest that this was a separate version of Alex from the explosion that survived, with the chance of The Atoner Alex returning in a later game.
Franchise Killer: Not only were the game's sales poor enough to cause the developer to say a sequel was out of the question, the poor sales led to Activision shuttering the developer that created it, Radical Entertainment.
Narm: The redesigned uniforms of the standard Blackwatch troops look rather silly.
The writer's attempts to make Blackwatch seem evil are so over the top that they almost seem like parodies at first, made more extreme due to the fact that they are supposed to be taken seriously. Yahtzee puts it best: "If you take the time to track down the collectible audio logs, you'll find that approximately one hundred percent of the things record someone at Blackwatch talking about how much he loves throwing schoolchildren into jet turbines and rubbing the greasy remnants into his prostate...you have to wonder where Blackwatch could possibly be finding this seemingly inexhaustible supply of emotionless psychopaths".
Narm Charm: Besides the Blackwatch evil seeming hilarious (possibly intentional), there's also Heller's side of the dialogue during the final encounter with Mercer.
Player Punch: You may or may not feel anything about the eventual fate of Luis Guerra since all he does is just feed Heller information and provide off-screen assistance, just that he and Heller knew each other for a considerable time by the start of the game.
Mercer's status, as well. When Heller finally kills him, the player gets to look out of Mercer's eyes while being eviscerated!
Play the Game, Skip the Story: Several reviews have reach this conclusion - the plot is simplistic and overwrought, but the combat and other gameplay is tighter and more polished than in the first game. Some fans of the first game feel this way too, believing the gameplay to be as good or better as the first, but resenting the story developments.
Replacement Scrappy: A subset of the fanbase does not like James Heller, more or less because he replaces Mercer as the player character.
Sequel Escalation: At least compared to the first game, this one has concepts from the Hulk game not available in the first. Also, the ways in which powers can cause massive havoc has gone up despite several moves from the original being trimmed if only because they didn't take things over the top even higher.
At the same time, it seems to be deescalation as well. In the original, it was hinted that if the virus ever got off Manhattan Island, the world (or at least North America), would be a lost cause. In P2, the virus spreads to the Yellow and Green zones (Manhattan is the Red Zone)... but its hardly game over. Additionally, Blackwatch's plan to destroy Manhattan in the original involved a nuke, while in P2, their plan involves slow moving, poorly armored helicopters armed with thermobaric weapons.
That One Sidequest: The divebombing Radnet events can be this, depending on how they're set up. In particular, one in the yellow zone is set up in such a way that you need pixel-perfect aim to take out an 'X' formation of targets in one hit. The corners are just far enough apart that you'll only hit two out of four unless you hit the target dead center, forcing a second dive to hit the stragglers. This makes it nigh-impossible to pass the third round, meaning you'll just barely reach gold.
While for the most part the gameplay is an improvement over the first game, the reworked controls and new abilities meant ditching numerous old ones, including multiple kinds of Devastators (only the Tendril Barrage can be used), Musclemass, Armor (hinted to be DLC later on, though this turned out to merely be cosmetic so it does nothing but make the character look different), Patsy and numerous Awesome but Impractical moves that're either superfluous or not strong enough for their intended targets.
Villain Decay: Blackwatch. In the original, they were portrayed as a fanatical unit of utterly ruthless killers who would and did shoot fleeing, unarmed civilians and each other if it fulfilled their objectives, and wielded frightening power in the name of containing any outbreak and any witnesses to an outbreak. While they still engage in dog-kicking left and right, perhaps to an even greater degree than in the original, they're harder to take seriously after a few Blacknet missions, such as the one where you're picking up radio transmissions from a trooper referring to everyone as "Brah", or when you realise they're now beholden to Gentek rather than Gentek being created, funded and heavily controlled by Blackwatch. One can assume they've had to lower their hiring standards due to the high, uh, turnover.
At one point it's mentioned that there are 10,000 Blackwatch personnel in the city. In fact, while playing the game you see more Blackwatch than regular Marines, which is an inversion of the situation in the first game. Although it's partially explained that Marines are still supposedly treated as Infected-fodder by being deployed mainly in the Red Zone while Blackwatch personnel try to keep their (and Gentek's) mischief under wraps by enforcing a regime in areas under dominant military control.