It goes back to Johns creative control and push of Cyborg in the comics at the expense of Martian Manhunter. So yeah it is Johns' fault.
Fair enough. It's a very minor issue for me though. There's so many other problems with the DCEU thus far that I'm just more focused on having a quality, coherent film.
With all of numerous film projects currently in development, I'm sure J'onn will appear soon.