I just can't believe that there's been 17 years worth of X-Men films, and they couldn't figure out a way to correctly set up and execute the phoenix saga. You can't just have Jean Grey get introduced in Apocalypse and all of the sudden go into Dark Phoenix mode in the sequel, that just won't work. The audience barely knows who she is and she hasn't had time to establish any kind of relationships with the other characters, especially Cyclops who is central to the arc in the comic books.
It's amazing that the best translation from the comic books to film is still the 1990's animated series. It's 25 years old and was made on a minimal budget, but still did a much better job of adapting the characters and story from the source material. Get your shit together Fox.
And God I hope Jen Lawrece does not return. Her character arc makes no sense in the current movies. She goes from "Mutant and PROUD!!" in First Class to barely showing her true form at all in Apocalypse. Fucking stupid.
That's not the problem. The problem is she goes from eye candy who can act, to Mutant terrorist to field leader of the X Men and pretty much saviour of the fucking world. Again, I love me some JLaw. She's a fine actress. But Mystique was never more than B List at best, and that doesn't change because you've got an A List actress in the role.
Mysitque's powers make her perfect for cool shit like spying and the occassional assassination. In FC, she only uses her powers once in combat, to distract Azrael by morphing into Shaw. By DoFP, Lawerence was one of the biggest stars in the world, so they basically wrote the film around her and made her central to the plot. It actually worked; Trask using her DNA to give the Sentinals their ability to adapt to Mutant's powers and kill them was a nicely creepy touch. The film was well written and stongly performed by a heavyweight cast.
But she should never have returned for Apocalypse, or at least not in such a prominant role. The idea that Mystique can somehow lead the X Men, most of whom are more powerful than her, into combat against a being like Apocolypse is laughable. Her greater, "experience" is irrelevent, since she mostly works alone to rescue other Mutants. She has no more experience of leading the team than Beast. Her powers are literally useless against En Sab Nur; the one time she tries to fool him, she gets rape-choked.
Of course, It's certainly not JLaw's sole fault that Apocalypse was a great, steaming turd of a movie. But she should still cut her losses from the franchise.
Oh, and the reason we rarely see Mystique in her blue form is that by the third film, JLaw was a big enough star to limit the amount of time she would have to spend wearing uncomfortable make up.