3) The Phoenix
During the film’s climax, Magneto’s efforts don’t hold Apocalypse forever, which means the X-Men have to turn to an even more powerful force to stop him – resulting in a fan-baiting tease of a future plotline.
After what Professor X told her earlier in the film about embracing the full extent of her powers, the conflicted Jean Grey unleashes her pent-up telekinetic abilities and seemingly kills Apocalypse in the process. The would-be destroyer of the world is awed by the sight and ambiguously says “it’s revealed” as he sees Jean’s powers take the shape of bird made out of fire. A phoenix.
X-Men fans will know that this is foreshadowing the Phoenix Force, the huge cosmic power that Jean possesses which eventually turns her to the dark side. This iconic storyline was disappointingly realized in X-Men: The Last Stand, but let’s hope they can do it justice if they tackle it again in the future.