I think the Wolverine part worked well when you take into account just the X-Men movies, but not when you take into account the Wolverine specific movies. More than anything I see this movie as Bryan Singer wanting to wrap a little bow on his time with the X-Men franchise, as it references almost all of it and ignores the parts he didn't have a part in (except a small reference to X Men 3).
I am ready for Singer to leave this franchise alone. His original thesis for the X-Men movies- make them good movies anyone can enjoy and forget about the comic book nerds- was great in 2000 before we had a comic book movie boom but in 2016 seems very antiquated. The week after I saw this movie I went to see Civil War, a movie PACKED with nods to comic nerds (like the Captain America speech as a eulogy, or Ant Man riding on a Hawkeye arrow, etc.) that made the movie BETTER for those who know the material but still fun for those that don't. All he needed to do was give us nerds one throw away scene (like have Apocalypse lecture the first person who sees him after he wakes up and asks if he is a mutant that "I am as far beyond mutants as they are beyond you!") and I would have been a lot more forgiving of this movie, but he didn't and that is why I would be glad if he never made another X Men movie.
I feel like that the only time we got to see Apocalypse as he should have been represented was when he and Prof X fought in the mental world and Apocalypse grew in size and starting crushing Prof X. That was the Apocalypse that should have been in the real world of the movie, not the regular sized blue freak that was trotted out as Apocalypse.