How Does Newt Fit Into The Story?
Ever since it was revealed that the sequel to Fantastic Beasts and Where to Find Them would be subtitled The Crimes of Grindelwald, and that it's part of a five-movie plan, it's been clear that the franchise will grow beyond Newt Scamander.
Eddie Redmayne's magizoologist is still important to the story here, but you can already feel him being pushed further to the side. The movie is more interested in The Crimes of Grindelwald than it is Fantastic Beasts, and that's only going to intensify as it builds towards the 1945 duel.
That means it needs to focus in more on Grindelwald's rise and dominance, alongside his relationship with Dumbledore and how he is eventually able to move against him, and now there's Aurelius to add into the mix too. It's so much bigger than Newt, but their commitment to using the Fantastic Beasts name means he really ought to appear in each film - it's just difficult to see how he fits in in any sort of major capacity.
How Does Queenie Come Back?
Contrary to the ending of the first movie, Jacob has retained his memories, and is still in a relationship with Queenie - although she has him under a love spell, so that he'll agree to marry her. Once that spell is broken, things rapidly go south, and by the end of the movie Queenie is not just receptive to Grindelwald's message about being free to love who you want, but actively joining his side.
It's an interesting idea, if not all that well executed, but it's also a means of keeping Jacob invested going forwards. He isn't simply going to give up on Queenie, which means the movies can't either, and she already seems quite well regarded within Grindelwald's inner-circle.
There are still three movies to go, so it's extremely plausible, perhaps even likely, that Queenie will switch sides again and love wins out, which would be thematically resonant with the entirety of Potter canon. It's not going to be that easy though, although Queenie's considerable skills as a Legilimens may come into use to. The other possibility is that this ends more in tragedy, with Queenie's attempts to turn back resulting in the death of her or Jacob.
How Does Nagini End Up With Voldemort?
As was speculated and then officially confirmed prior to release, Claudia Kim's Maledictus character is indeed Nagini.
Cursed to one day permanently transform into a snake, we know that her ultimate future lies at the side of Lord Voldemort, but this movie doesn't give us any hints as to how she might end up there. She wanted Credence to stay with her rather than go to Grindelwald, which shows that at this point she has no inclination to align with a dark wizard, so how does she end up becoming one of the Dark Lord's most faithful companions?
Why Was McGonagall Already At Hogwarts?
Minerva McGonagall's backstory wasn't really touched upon during the Harry Potter series, but through Pottermore - which comes directly from J.K Rowling - she has been fleshed out further, and we know a few key facts about her. The most crucial and relevant to The Crimes of Grindelwald is that, as of 1995, she'd been teaching at Hogwarts for 39 years, and that she was born in 1935. So how, exactly, is she already teaching at Hogwarts in 1927?
The potentially canon-breaking inclusion of McGonagall was revealed before release, and the film does nothing to clear the matter up. She is simply, matter-of-factly, a teacher at Hogwarts who is approximately in her 30s. On top of that, Dumbledore is banned from teaching Defence Against The Dark Arts in the movie, which is presumably how he ends up teaching Transfiguration, but what does that mean for McGonagall? Does she teach DADA, or some other subject, in a move that's never been mentioned before, only to return to Transfiguration when Dumbledore becomes Headmaster? Her role in the movie is minor, which suggests it's not even supposed to matter all that much but, as with other elements, it's indicative of Rowling's new approach to canon, and one that's likely to divide fans.