I doubt he'd want to move from directing 3 big fantasy movies in a row to directing 2 even bigger fantasy movies shot simultaneously! Don't think he's right for the LOTR universe anyway.
I think they probably already have a new director lined-up, maybe even before they officially announced del Toro was leaving. For me Alfonso Cuaron would be the ideal candidate. He's a friend of del Toro's so that would certainly help the transition from one director to another, as well as keeping del Toro's involvement open, which it should be even though he won't be sitting in the director's chair at the end of the day.