[Prototype] was one of those games that was shadowed by many due to Infamous being released in close proximity to it. It had its flaws, but nothing that prevented the game from functioning. The problems that I experienced were too many flying scan-bots and some of the side challenges were just unrealistically hard.
[Prototype 2] is much improved, the main character James Heller doesn't have to waste much time figuring out what happened nor does he seem to care. In the beginning his only concern is finding Alex Mercer, the first prototype, seeking revenge for the murder of his wife and child. It is a simple yet powerful driving force, and when he gains his prototype powers he questions nothing, unlike Mercer who had lost a vast amount of his memory in the first installment.
The story is fairly easy to follow, and I didn't find myself constantly saying "what does that mean" like in the first game, which was more of a mystery theme. The city setup is easy enough while using the standard GTA style gps and mapping feature.
The controls are much the same as the first title but so are some of the powers, they also utilize an ability wheel like many games are moving towards when multiple selections are available. But they achieve a good balance of use. No one weapon works well on everything, which is a balance that [Prototype] didn't fully achieve. Of coarse each player will develop their favorites. Mine was the tendrils.
They did remove the side challenges from the main game, but they seem to be available with the online features and it seems that they will have weekly additional challenges.
Overall I like this game more than the original. It felt better.
As for trophies in this game I am pleased to report that there are no ridiculously impossible ones. The most difficult one I think is to beat it on hard which just requires a second play through if you don't start on that difficulty.
Overall this sequel fixed many if not all of the problems the first one had, although a fairly short game it felt very complete.