I've never been overly impressed with the "Dark Phoenix Saga". However, done well for film it would be best as a character piece about Jean Grey starting to lose herself as her increased power and the sensations she gets from using it for destruction cause her to lose control. All of this leading to a final conflict. When they did it in X3, it was about Jean having a split personality and whether or not Wolverine would stab a woman he had the hots for.
I don't think it's necessarily the story's fault as much as it's Fox's fault they can't seem to shift focus away from the characters they think are the "stars".