Imo it feels like these writers don't juggle different parts of a story all that well.
First film gave a lot of focus to the underlying story, but the Turtles lost out a lot.
Second film reversed it while they focus on giving the Turtles a lot more attention like they should (and I like this one better because of that), but the main plot falls very weak and seems clearly rushed half way through.
They can do okay/better on one thing, but not the entire thing...