Prototype 1 was generally regarded as well-intentioned but an overall disappointment (critically and commercially). Yet it has a solid 4-star rating on Amazon while P-2 only has 3.5. Is it really worse or is it simply too early to tell?
I think Prototype 2 is better than the first in general. Then again people have different tastes in games. There is more area in the game, but probably not by THAT much. You can actually "stand your ground" on most, if not all boss fights instead of "hit and run" compared to the first. Some ratings are probably tied to the dislikes they had with the game. As you know, games and their sequels cannot be exactly like each other.
Prototype 2 was definitely better than the first one. I saw a couple very negative reviews and it didn't look like the reviewer even played the game. I enjoyed the first one, and loved this new one. I would recommend if you liked the original.