Probably trying to move a little closer to the novel continuity, in which Ellie marries someone else between JP and TLW. However in JP she was engaged to that person, so the films had already deviated. Does seem a bit odd. Maybe someone decided they didn't want Laura Dern to be a lead character for some reason.
:edit: Or maybe she decided, as a big shoot and publicity junket means a very long time away from home.