What I think is that it could very well be a follow up to Minus One but not a full blown sequel. What I mean by that is that it takes place in the same continuity, but there is a major shift in the focus of the story. Instead of following up directly from the loose plot thread about Noriko and Godzilla's regeneration, there is not a direct explanation for any of that.... yet.
Instead, something like the emergence of another Kaiju like Hedorah, Angurius, or an original monster focuses the character's attention as well as Godzilla's. Then, after the fallout of that film, more pieces of the puzzle fall into place for a third and final film to tie it all together in a perfect trilogy.
Think the Dark Knight trilogy. Batman Begins focused on Batman facing the League of Assassins, but then, in the Dark Knight, the focus shifted onto the Joker until Rises where all of the plot threads came together.
