They'll probably kill Xavier, Magneto, and Nightcrawler. Given that Ian McKellen and Patrick Stewart are the big cash guys. And this way they can always bring them back as younger characters, if they want. As for Nightcrawler, the studios were pretty vocal about not wanting Kurt and Beast to be similar at all. Hence why Kurt has no velvet fur. But he could still be the one targeted for death.
As for who gets left powerless in the end? I'm gonna go with Jean Grey. Originally the Phoenix saga in the comics ended with Jean losing her powers instead of dying. This was to lead into a long storyarc, and with Magneto popping up for the 200th issue to give Jean back her powers. This of course never happened, cause Marvel head honcho Jim Shooter would not allow Jean to live, after killing Millions. Hence the later retcon that it wasn't really her that was the 'Phoenix', and her real self was in a cocoon in the Bay.
MTFBWY and HH!!
Jar Jar Binks