3) Dark Phoenix
Bryan Singer has recently spoken on how he would love to tackle the Dark Phoenix Saga, and so there are many easter eggs in Apocalypse that suggest the Phoenix is Jean’s fate in this revised timeline, too. In particular, Jean’s talk with Charles about being afraid of her powers and the eventual display of her abilities as a fire bird obviously point to the Phoenix Force.
As well as the Phoenix references, there are a few other callbacks to previous X-Men movies scattered throughout. When Havok and Cyclops turn up at the X-Mansion, Charles is quoting The Once and Future King by TH White to his students. This is the same book that Magneto reads in his cell in X2.
Likewise, Charles and Erik’s final conversation, in which the Professor warns “I feel a great swell of pity for the poor soul who comes to my school looking for trouble,” is lifted from their talk at the end of the first X-Men.