Continuity mistake: Despite having the Phoenix power at the end of X-Men: Apocalypse, which manifests around her as a Phoenix firebird and she uses to defeat the titular villain, Jean Grey doesn't actually get merged with the entity until 9 years later in this movie.
Dark Phoenix (2019)
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Directed by: Simon Kinberg
Starring: James McAvoy, Jennifer Lawrence, Jessica Chastain, Sophie Turner
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Suggested correction: Jean used her full psychic powers in the previous film, not the Phoenix Force. Even without the Phoenix Force she was an incredibly powerful, Omega Level mutant.
The Phoenix firebird is literally shown to be emerging from Jean's body when she kills Apocalypse. She can't both have the Phoenix firebird already within her and then somehow also have it invade her body in this film. The mistake is valid, and I would argue it should be listed as a plot hole more than a continuity error.
Ororo Munroe: Sometimes, you want to believe that people are something that they are not. By the time you realise who they are, it's too late.
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Question: Some valid reason Mystique dies early? Did Jennifer Lawrence get tired of playing her and wanted out?
Answer: Your guess is correct. Lawrence stated she was done with the franchise after "X-Men: Apocalypse." She jokingly told Simon Kinberg she would return for this film if he directed it, and to her surprise, he was serious about it and held her to it. Fans weren't very keen on her appearances either, because she was definitely phoning it in for the third film, so that may have factored into killing her off early as well.
More than one actress had played Mystique. Just because Jennifer Lawrence did not want to continue playing that role is not a reason the character would be killed off. They could easily recast another notable actress in the part. I would not be surprised if Mystique is miraculously "resurrected" in a future X-Men film with a new actress.
Aside from Deadpool, any new X-Men film would be a complete overhaul of the franchise since the characters will be part of the MCU now. You're not wrong about an actor wanting out to not really be a reason to kill off a character, but it doesn't preclude them from doing so either. They might have decided it wouldn't be worth the hassle of recasting the role with all the negative baggage that would come with it.
Here are some candidates I think could do it: Amanda Seyfried, Shailene Woodley, Chloe Grace Moretz. Heck maybe even Milla Jovovich-Anderson should be given an audition, what say you guys?