The ending resolves the New York crisis and plants the conflict that the two sequels pick up. After Grindelwald is captured, Newt's Thunderbird releases a rain over New York that erases the memories of ordinary people, and the wizarding authorities repair the damage and hide all signs of what happened.
Why does the memory rain matter? It is a cover up on a city scale, and it echoes the main saga, where the Ministry of Magic spends Harry Potter and the Order of the Phoenix denying that Voldemort has returned. In both stories the wizarding authorities protect secrecy before they protect the truth, and in my opinion this is the clearest thematic link between the two series.
What does the Occamy eggshell scene mean? Newt leaves Jacob some eggshells from a creature called an Occamy, which Jacob sells to open a bakery. When Queenie visits the shop, her presence brings back his memory of her, and he smiles. It could be argued that this is the warmest beat in the film, because it shows the memory spell has a gap, and it gives the story a quiet payoff that does not depend on a spectacle. Jacob is also the only No-Maj to walk away with something, which sets him apart from the Muggle characters of the main saga, who are mostly kept in the dark.
What does the exposure of Grindelwald set up? Graves turns out to be the dark wizard in disguise, and his arrest puts the villain in custody at the close of this film. That makes the film feel closed, yet Fantastic Beasts: The Crimes of Grindelwald opens with Grindelwald escaping custody in 1927, as he is moved from America to Europe for trial. Credence is thought to be in Paris in that sequel, which suggests the Obscurus destruction in the subway tunnel did not end his story, and the later credit of Credence Barebone / Aurelius Dumbledore in Fantastic Beasts: The Secrets of Dumbledore confirms it.
Compare this with Harry Potter and the Sorcerer's Stone, where the opening film leaves the villain's story unfinished. Here the villain is caught, and the open thread is a boy. Perhaps that is the film's boldest choice: it ends on a happy note for Newt and Jacob while leaving its two biggest threats open.