Platforming and level design was good and not frustrating or boring.
Music was magical.
Enemy AI was terrible, the gunman were interesting in that they would avoid bullets, but otherwise underused.
As for the story... Let me get this straight:
A Man in a post-apocalyptic world goes on a sociopathic rampage against the one group of people working to save humanity, and utterly destroys both them, an all their progress, further damning the world to its already miserable fate. Humanity might go extinct without their work for all we know!
I understand hm wanting to save his daughter, but in the begging when they took her, he automatically assumed that she was being taken away from him, and going to be hurt, so he freaked, and got shot.
But he lived in that world. He knew how terrible it was. Surely he understood the importance of what they wanted to do, and based on the dialog in the game he seems capable of rational thought at the very least. Couldn't he just have asked to go with them so he could have been with his daughter during this? They had the means to hold both of them.
His reaction isn't totally unfounded, as a parent, someone coming in and saying they want to study your child would be confusing at best and terrifying at worst, but he could have asked questions, gotten a clearer picture of things, after all, it appears they had no intention of hurting her. You don't need to carve someone up for a tissue sample.
The game tended to tote the player character as the hero. A good guy out to save his daughter.
I saw him as a lunatic ready to murder anyone who stood in the way of what he wanted.
Even if what he wanted was tied to him through bonds of love, it was the hero who was truly the destructive Machiavellian force in this game.
It is for this disparity between what the game is at what it says it is, that I cannot rate this higher.