For you to introduce a foreign enemy, I think you also have to develop the struggle at home first. So Apocalypse should have started out with the mutant/human conflicts at an international scale, just to remind us what the premise of X-Men is.
Apocalypse should have made an appearance halfway through and should have only been foreshadowed before (Singer is good at this: Recall the scene in the plastic prison cell: "Doesn't it ever wake you in the middle of the night, that they will come and take your children?" leading to the raid in X2). Religious references, alien references, etc. Bring in some researchers, maybe they've found mutant DNA on a meteor, whatever. As long as Apocalypse is not so random in the X-Men continuity (which he is).
Then there's the fact they never linked DOFP to Apocalypse. Asimple acknowledgement of the time travel in DOFP would've done. Just something subtle to understand Apocalypse is a result of time travel, maybe Apocalypse saying that he was awoken by some fool's tampering with space-time? He'd have an archaic way of putting it.