Who knows. He never popped his claws after coming back, so we don't know if he has them or not (though I admit, one of the funnier scenes I saw was Wolvie walking through the metal detector, it not going off, and the look on his face).
Mystique's always been taken with the preservation and proliferation of the mutant species. I can see her experimenting on Wolverine much like Stryker would have. To make "the ultimate defender of the mutant race" of course, though.
