Phil: My guess is that Xavier is just in his head, and doesn't actually exist anymore.
Even though we see him in the truck with Logan and X23, when it's spinning out of control? (Still could be in his head, sure... but to me, it seemed like he was there... because I have a feeling, at the end, when he's holding the shovel, that's him burying Professor Xavier... and I have a feeling whatever happened to Prof X, probably half way through the movie, will be the turning point for Wolverine, where he is forced to go after the Reavers, Donald Pierce, and whomever else...)