Bayona has exited World War Z 2 because of prior commitments directing A Monster Calls, the dark fantasy film opening later this year and starring Liam Neeson. Although wrapped, Bayona reportedly still has "pre-existing" commitments that will keep him from taking on the zombie sequel which Paramount wants to get moving on quickly. Here's the official statement released by the studio...
[Juan Antonio] Bayona is no longer able to make World War Z 2 this year, and it is our ambition to do so. He is a wonderful director and we hope to work with him soon.
But is that the only reason he left? A few months ago Bayona was the favorite to direct Jurassic World 2, but couldn't because of scheduling on A Monster Calls. If the timing can be worked out that is a likely destination for Bayona's next film.
As for World War Z 2, Paramount needs to find a replacement quickly if they intend to hit the June 2017 release date. [Deadline]