1. Storm, Jean and Cyclops were not born at different times. Their ages are the same, even if Jean looks younger in the flashback in X-Men: The Last Stand. There are no discrepancies here.It is like if the X-Men universe were 4 or 5 different universes that Fox insisted were the same continuity:
-The original trilogy
-The Deadpool movies
-The New Mutants
-And every Wolverine movie is part of a diferent chunk of the universe: the Origins is a similar but not exactly indentical universe of the original trilogy, the Wolverine is a original trilogy movie and the Logan movie is a New Mutants universe
And yes, I know that technically, the original and prequel movies are diferent universes, but they present continuity discrepancies that are not explanable with time travel, like Storm, Jean and Cyclops been born at diferent times and Apocalypse arriving without explanation of why he didn't arrive in the other timeline.
2. Apocalypse did not arrive without explanation. He was trapped and only freed in the Revised Timeline.
I'm sure I could easily resolve most issues people have with the small inconsistencies.