MovieWeb is stating that Benicio Del Toro could not come to a deal with Paramount on the JJ Abrams Star Trek sequel.
In addition, they state that Khan is, indeed, the villain.
Abrams was just asked if Del Toro was playing Khan, to which the director replied, "Not true."
Seems he wasn't lying.
The as-of-yet unnamed Star Trek sequel is due in theaters May 17th, 2013 in 3D.