Prototype 2 is a great game. I enjoyed the story. I feel that the way powers and abilities are handled works well for causing a rounder character without making the player feel blocked. In this article, major spoilers are visible by mousing over the black boxes like this. (note that mobile devices shows all spoilers. sry)
The first annoyance that I had with the game involved the claws power when using the pounce ability. The camera would decide to go action style and throw the viewpoint behind the enemy. This was often disorienting at best and increased the difficulty of the game by preventing intelligent dodge mechanics from being used at worse.
Whenever Assassin's Creed did this, it was to align the animation so that Ezio's attack looks fluid and normal. I assume this is the same reason Prototype 2 does this. Ezio gains immunity to damage during this sequence, where Heller does not.
Soon enough, I learned that holding the joystick to the side while smashing dodge was the only consistent solution to avoiding damage when the game did this.
My second annoyance comes from the final boss in the game. I feel that suspension of disbelieve that Heller has any chance of killing Mercer is lost when during an attack combo I am dealt damage and moved back into the arena without any chance to dodge or get out of the attack.
This happens to me as I'm using an attack to deal damage to Mercer and I'm still floating away. I then follow this with a claws attack. Yet the player crossing the invisible wall has Mercer dealing a free hit on the player via long whip. This significant damage on a stick without chance for dodge tells me that Mercer could kill Heller whenever he pleases. (Yes, even after the third round when Mercer starts getting his ass kicked.)
Blackwatch, the military power of the game, holds my third annoyance. If the player attempts to go too far north of the red zone, the player is instantly killed by Blackwatch weapons. If Blackwatch had these dot die focus damage weapons, why didn't they use them sooner?
I can accept in such a scenario that a player starts taking damage from a perceivable force while walking into a zone the devs don't want the player in yet, and stopping the player at some point in this damage zone with an invisible wall, gradually increasing that damage. Alas, in this case flat killing the player doesn't make sense to the power of the player vs the abilities of the enemy.
After all of this, the game is still a great game and a great buy. Onto my final annoyance which comes from either the publisher or the developer. There is content that existed in the original game that is not accessible to players who purchase the game used within the second game. This includes all of the events and challenges that had medal rewards from Prototype 1. The inclusion of an online leader board and/or extra dlc content unlocked by completing these radnet events is cool, but denying the base single player content to players who either borrow the game, or purchase it used makes this game will not buy for me.