How do you think it was done using FCS? I was thinking they actually created the video game character so they had access to his behavior. Even so, how could you get him to move inside the video?
the only way you could do this in FCS is if you were able to capture video of the character making those exact movements and precisely masking the elements. This was most likely done with a combination of a 3D modeling program (like Maya, SoftImage, etc) and a compositor (like Shake, After Effects, Combustion, etc).
This could be done in Final Cut Studio, but the video would probably take months. Placing a 3d character in a scene is hard stuff especially if the camera is moving as it is in this one. They had to do some serious camera tracking for this.