In a recent interview with Cinema Blend, Simon Kinberg (writer and producer of X-Men: Apocalypse) said that he and Bryan Singer always intended to feature Wolverine in the latest X-Men installment. And that is no surprise to anybody, since Wolverine is the most recognizable character in this shared universe, and the same actor has portrayed him throughout all of the franchise’s installments.

This being said, Kinberg also revealed that Wolverine was, at first, intended to have a bigger role in the movie. Thus, he was supposed to appear in the middle of the movie and be something of a drill sergeant over the young mutants. But this interfered with the plan to give Mystique a bigger and more central role. And thus, Wolverine was relegated to appearing in a simple cameo.

And it was for better and for worse, at the same time. While it would have offered the opportunity of to explain his last scene from X-Men: Days of Future Past, it would have robbed the viewers of the opportunity of seeing one of the best scenes in the entire movie - a raging Wolverine, straight out of the comics (obviously, still PG-13).

So, in a way, it was decided to reiterate the character’s origin story of the character and combine it with the movie’s rescue mission. Thus, the scene felt organic and more in touch with the character than it would have felt if Wolverine had acted as an instructor for the young mutants.

Still, there is one big question still remaining after this decision was made. And that question is related to the shape shifter who captured the mutant at the end of Days of Future Past. However, as Kinberg said, the credits scene of X-Men: Apocalypse leads directly into the third and final Wolverine film to feature Hugh Jackman.

So it will all be explained with the 2017 release of the third Wolverine movie.