Ya, the story in Prototype 2 was trying too hard to be taken serious. I too did muse on the fact that Heller kept saying "I will save all the innocent people being turned into infected, by the cruel and merciless Mercer and Blackwatch!" 2 minutes later you're chugging down these innocents for health and fun.
The leveling up system, or rather, the skill points and perks in this game I felt was a bit stupid. Most of the perks were double ups of each other in different talent trees, which were pretty "unimaginable" imo, when compared to the rest of abilities you have. Why not get a talent tree which would make your attacks a bit more "unique" perhaps, adding a second effect maybe on the black hole tendril attack?
Other then that though, I did have lots of fun in the game, roaming about body surfing on people and such!
EDIT: And using the claw abilites were much more satisfying in this game imo, along with the tendrils or hammerfists. Still sad they removed the hammertoss ability, was fun to use. :<