Looks like Toho wanted that sweet Cinematic Universe money and decided to cancel Shin Godzilla 2 and will probably reboot the franchise again for long-term plan this time.
I loved Shin Godzilla, yet I'm perfectly okay with this decision. Making Shin Godzilla a standalone one-and-done movie is better than risking to continue the story only for it to go downhill or fall off a cliff (like what happened to the original Showa Godzilla after the first 1954 movie). All in all, I'm very grateful that I was given a chance to witness Hideaki Anno's take on Godzilla in my lifetime, and now, with Shin story (reportedly) done and possibly won’t be revisited again, hopefully Anno can start working on the final Evangelion Rebuild movie. We've been waiting years for it.