What I got out of the ending was that Alex Mercer is nothing more than the Virus itself, but when he consumes someone, he gets everything, from their appearance to their memory to their body mass, which is where his shapeshifting comes from. This is gonna be a fight that relies entirely on technicallity. It's been shown that Xavier has a very hard time manipulating alien's minds, but Alex is made up of human parts, and most likely stores his memories in them.
Is his sentience also developed through consuming others? If so, I'm going to guess that he's reliant on the human parts that he consumes to enough of a degree for X to manipulate him.Considering at the time he woke up he couldn't remember anything until he ate one of the guards following him, I'm a guessing yes.
