Okay, so there's 7 things that could salvage this movie.
1.
Make it a two-parter. The Dark Phoenix Saga in the comics was built up to for years, and there was a lot of storyline that would have to be skimmed over or left out unless they wanted another bloated mess like Apocalypse on their hands. I would have the heroes deal with Sinister or the Hellfire Club in the first movie and have Jean go bad at the end of that one. In the second movie, they could delve into Jean's cosmic rampage and all of the Shi'ar/outer space stuff. If they rush this installment, it'll be X3 all over again.
2.
Make Scott and Jean the focus. They messed up X-men 3 by trying to focus the whole thing on Logan when Scott and Jean are who the story was really about. We need to see Cyclops shining as a true leader, and we need to see Jean doing her thing too. They need to get us invested in these two characters, because their star-crossed romance are the true heart and soul of the whole thing.
3.
The streets aren't feeling Mystique like that. Stop trying to make her a hero
This was the most annoying thing about Apocalypse, IMO. They tried so hard to make her a hero because she's played by somebody. It's way out of character and makes no sense. I would have her return as the leader in this movie only to betray everyone within the first 30 minutes. Have Mystique reveal that she's been working for Sinister all along and sell out the group. She could serve the same role that Jason Wyngarde did in the comics by using trickery and deception to manipulate Jean for selfish reasons. Because that's who Mystique is. A villain.
4.
Use Sinister as the villain since he was built up in the last one. I'd rather see the Hellfire Club, but they all died in First Class.
But still, Sinister is the last of the major villains we haven't seen yet, and having the heroes fight him and Marauders on the big screen would be a real treat.
5.
Bite the bullet and recast Wolverine. He's way overused, but too iconic to be left out of such a major story entirely. Essex Corp was collecting Wolverine's blood in the last one, so that gives them a reason bring him back with a new actor. The clone wolverine could start off working for Sinister and switch sides halfway through.Behind Scott and Jean's last stand on the moon, Wolverine vs. the Hellfire Club goons was the second most iconic moment in the whole story. Even if they use Sinister, Wolverine getting that Dirty Harry moment against the Nasty Boys would be
6.
Give Magneto a break. He's a brilliant character and Fassbender killed the role no doubt, but when he's the villain in every movie, and has the same arc in every movie, it gets... old.
On top of that, Magneto had nothing to do with the Dark Phoenix story at all in the comics or the 90s cartoon. Let some other villains shine for once.
7.
We need to see the whole team working together. I want to see Storm, Nightcrawler, Cyclops, Jean, Wolverine, and Beast all doing work together as a team. Nobody's interested in seeing X-men: [insert big-name actor's name here] and some other guys: the motion picture anymore in 2017
This could be an opportunity to showcase some other characters as well. They could handwave Angel's "death" in Apocalypse and have him join the group anyway between movies, or introduce a young Colossus, since both of them were in the original comic storyline. Maybe include Rogue and Gambit instead just so the 90s babies will want to see it. Either way, we need to see the team working together
(I like Quicksilver, but I would probably leave him out. They could say that he left to go searching for his dad. He's a cool dude but way too powerful to be a regular team member IMO).
Note: I'm not holding my breath for any of this to actually happen. A breh can dream though.
(I'm not holding my breath for this, but it could be dope if it wound up happening.)