In addition to my above post on how X-Men: Apocalypse hurt Dark Phoenix, the reason Dark Phoenix works as a story is because of the attachment the audience has built with Jean, Scott, etc. We've been reading their exploits for years and we desperately want to see them save Jean from this dark force within her. But, X-Men: Apocalypse opted to not serve the young X-Men they introduce. Therefore, they're underdeveloped. Why do I care about Jean going all Dark Phoenix if I never cared about this version of Jean Grey, Scott Summers, etc in the first place? The Dark Phoenix in X3 at least had the OT cast and 2 prior movies going for it, so people cared more going in. Here, they just expect the name Dark Phoenix and Jean Grey and such to mean something, when the fundamental core of the story requires a level of character loyalty they haven't earned yet.
It was a mistake to use this storyline at this point in the franchise. It feels like old hat and recycled use of idea mixed with apathy towards these characters. This was doomed from the start. They needed an entirely new idea for a 90s X-Men film.