First off, I don't feel that the story is explained well enough. The game takes place three years after Nomad and his merry bunch head over to the Island to help Prophet destroy the aliens. So what happened? We get a few disjointed flashbacks, but nothing very revealing! And by how the story progresses, its like Prophet just got back to New York around the time Alcatraz landed. So what took Prophet so long to get to New York, did he swim all the way back?
Another issue I have is that I don't like the lack of familiar stuff (aliens, characters, ect). The aliens are suppose to be the same as the ones from the spaceship, but these new ones are a completely different in every way! Instead of being completely alien beings with sleek black exteriors that fly, there are now these chrome plated squishy things that walk. Why would they ever give up flying? That was fundamental to everything that they were! I know this is a minor point but the aliens color bugs me too. The Crysis aliens had a blue motif going on which gave them a unique atmosphere, but now they are nothing but red. Is that some kind of mood lighting going on there?
[Spoiler alert]
As for characters we never see a familiar face throughout the game other than Prophet! I want to know what happened to Nomad, Phyco, and Rosenthal!
Another thing that I miss from the first game was the ability to explore the extensive maps! For me that's what made Cyrsis special. But in this new game, you can only go where your supposed to go. There is no room for creative navigation.
In the end the game was kind of fun. It's unique in its own way, but it's so far removed from the first game that it makes me feel alienated.