If you were a big fan of the first Prototype this will be a let down.
Here is the big things that stood out to me:
The Environment
I understand with this being a new game it needs to have a new story line, but one of my favorite things about the original was that it started in a normal world then slowly built up. Something about being a hidden monster in a otherwise normal world was awesome, you could be walking down the street and then suddenly BAM!, you chuck some lady down two city blocks into a wall. Instead your left with everyone coughing with what seems like the SARS virus and they don't really care about whats happening to their world.
Blackwatch and Military Presence
This somewhat ties into the first, but I liked again how much more realistic it was with what seemed like a real Military presence. The Blackwatch characters in this one seem more like a cross between a Cyborg and Shredder from Ninja Turtles.
Monsters
These new bad guys are unoriginal and look like they are filled full of lava. It's almost like they took the original virus infested bloody villains and said "How can we slightly change them and make them kinda new but really lame looking."
The Gore and Cruelty
My favorite thing to do in the original game was to act like King Kong and grab someone out of a crowd run to the top of a building and then do one of his gnarly consume moves where he smashes some poor civilians face in with his foot or knee. The consuming in the new one only lets you do the gnarly bloody consume moves to the military guys instead of everyone. The consuming is also very lame compared to the old one, instead of it being super bloody they focus more on the tentacles.
Leveling Up
This may be more of a matter of opinion, but I liked how you could save up your points like money and then pick from a menu of power-ups. I don't like having to complete missions just to level up, I want to be able to kill anybody to save up and buy new moves.
One thing I like so far
The camera angles are pretty cool, I was complaining a little less when I got his claws and performed the "pounce" move. Target someone, run up to the top of a building and then hold X. Flying down from the top of a building with arms wide open to just slice some dude in half is pretty awesome.
Overall this is not terrible, just a let down from my expectations. I was very excited about this game and was looking forward to it the first time I heard word of it. I will still finish the game because it is still fun, just not as cool as the original.