Her trajectory at the end of First Class was her joining Magneto's brotherhood.
DOFP didn't follow that "trajectory."
No, that's not her trajectory, that's her team affiliation at the end of the film.
Her character arc's trajectory was gradually fully accepting that she was a mutant, not rejecting it at all, and to embrace her abilities. It was a story of empowerment for her.
And where does DAYS OF FUTURE PAST pick up? With Mystique continuing Magneto's war against humanity after the Brotherhood has been killed/disbanded/imprisoned. Clearly headed in a similar direction to her character's trajectory at the end of FIRST CLASS.
Her trajectory at the end of DOFP was she saw the evil of her ways but wasn't going to align with Xavier either. Apocalypse didn't follow that "trajectory."
It absolutely does. APOCALYPSE opens up with Mystique no longer attacking humanity and undermining mutant/human relations, but now serving as a covert mutant freedom fighter, more concerned with rescuing mutants who are being mistreated. She's now moving back toward Xavier's goals and vision as the film progresses. Reluctantly, but that's her character arc.
Where does APOCALYPSE end? Oh. With her aligning with Xavier.
In Apocalypse she was all-in on the mission to Cairo, when Cyclops tells her he can't control his powers telling him "Then don't!" The movie ends with her saying they weren't kids any more, they were X-men.
Now in Dark Phoenix Mystique is supposed to be the voice of reason, she's now the responsible one and Xavier is now the one pushing the kids to their limits. But she was the one that brought the kids to Egypt.
No this is not her trajectory.
That's because she gradually changes her mind about a militant approach with the young X-Men, about them using their powers to fight for their cause. It's literally her character arc. That's why her serving as their drill instructor at the end of significant. It represents the shift in her ideology that took place over the film.
She's not necessarily responsible...but she is experienced compared to the others. She seems willing to risk lives and exposure for the greater good.
And what else are we going to see in DARK PHOENIX? What's been talked about, in terms of the trajectory of the team itself? A more public X-Men. Which is what she was initially rejecting at the outset of APOCALYPSE. Gradually moving toward Xavier's vision.
This is reductionist. Many characters in the X-Men universe have switched sides. It's the nature of the gray areas involved in the ongoing mutant/human conflict, and a classic element of the X-Men mythology, moreso than perhaps any other superhero mythology.
Mystique's arc in the prequel films may not be comic book accurate, but it has been well drawn, well developed, and fairly consistent in its exploration of a character learning to balance her militant tendencies for the greater good.