I think there are a number of stories going on in the film, with some limited in scope to the movie, and some working on a much larger scale.
The Obscurus thread is part of the main Grindelwald overarching story that pits Grindelwald (antagonist) against Newt (protagonist). It's unclear which part of Fantastic Beasts is the subjective story because there are several possibilities. Once the second film comes out I imagine that will be cleared up. Newt is likely the MC, but I don't think this story has fully locked in yet. It seems we're on the precipice of an inciting event for the series story, or Grindelwald's capture IS the inciting event.
SERIES STORY BACKSTORY or SETUP
Fantastic Beasts begins with the final parts of the backstory/setup. I think Mary Lou Barebone is the Steadfast IC and Credence is the Change MC. Their SS is their abusive mother/repressed son relationship. The Obscurus attacks and the potential exposure of the existence of magic to the muggle world is the OS throughline.
RETURNING THE THUNDERBIRD STORY
This story has Newt coming to America to return the thunderbird to its home and is complicated by the escape of several magical beasts. Newt is the Steadfast MC and Change IC Tina. The SS is their budding (unfulfilled) romance. It is possible that this is supposed to be the subjective part of the main story, but it seems to be too independent from it to work (IMO). It may, however, be the beginning of a larger subjective story,
NOMAGE IN THE WIZARDING WORLD STORY
The last of the stories I see floating around in Fantastic Beasts is about a muggle made part of the American wizarding world. The MC in this story is Jacob Kowolski, a wannabe baker, who wants to open a bakery but doesn't have the funds to do so. He gets wrapped up in Newt's efforts to recover the escaped magical creatures, which mixes his thread with Newt's "Return the Thunderbird" story. However, in this story, the IC is Tina's sister, Queenie, and the SS is the budding romantic witch/nomage relationship between them.
I think the movie is not as successful as it might otherwise be is because it is doing a LOT at one time. Teasing out the above story threads shows why the story seems to end, then keep going, then end again, and so on. It also explains the multiple parallel threads being juggled back and forth. While this is easier to do in a book, it's only partly successful in the film. My hope is that much of this will pay off as the series plays out and once all is revealed, the complex beginnings can be seen as just that -- beginnings of multiple, fully-realized, intertwined stories.