I feel that X taking for Fantomex body and the way he is acting is how most people would act if you spent years trapped in what equates to mental limbo with a mad man. What is so great about Soule's story is that he is setting up psychological aspects with Charles that should carry over into very huge character developments.
We have a man who was originally defined by peace, unity, and turning the other cheek coming back from years of fighting for his own sanity in a sense. He has probably seen his students and loved ones die several times overs in the scenarios him and the Shadow King has played out. It's even possible in some of those scenarios Charles himself did the killing just to stay dominant or on even footing with his aggressor. What we are seeing now is possibly a Charles Xavier, after years of battling, who is now somewhat numb to the previous ideals he use to hold dear, possibly to a degree that he is wondering why he is even fighting for them at all. The fact that he was so cool with taking Fantomex's body is just another example of that.
All of which is amazing story material and character exploration that should be LOADS better than....
"Well here is Grandpa Chuck again everyone. Same Hero, New Wheelchair! Watch as he tries to interact with his battle harden students searching desperately for a place among them and then slowly fades into the background of his over crowed mansion."
Been there ,done that, and saw all three movies. This could be the Charles Xavier that everyone always wanted but never even knew it, if handled correctly. This could be front line Charles, a practice what he preaches Charles, and if nothing else a Charles that will make a lasting impression.