In X-Men: Apocalypse movie, when Apocalypse gained control of mankind, he simply used that superpower to destroy all nuclear weapons. At that time, I thought that he was going to enforce peace to mankind (maybe, by taking away freedom, as he was villain).
But later, we saw that he was actually going to use Magneto to destroy most of the mankind (non-mutants and weak mutants). If that was the case, why didn't he simply use those nuclear weapons to do the job?
You've fundamentally misunderstood his plan. Apocalypse' goal isn't to destroy humanity or cleanse the Earth of life. His primary aim is to return humanity to a state of bronze-aged barbarism so that he can rule them as he did when he was in Egypt.
Apocalypse: ... I was there to spark and fan the flame of man's awakening, to spin the wheel of civilization. And when the forest would grow rank and in need of clearing for new growth... I was there to set it ablaze. ... Everything they've built will fall! And from the ashes of their world, we'll build a better one!
His idea of an ideal society is that of the Old Kingdom (around 5000 years ago).
Storm: Where did you come from?
Apocalypse: The time before man lost his way.
He recognises that even with no weapons to oppose him, the world is simply too cosmopolitan to be dominated.
Storm: You can't save the world, just going around killing people. There's laws, system and place for that kind of thing.
Apocalypse: My child, why do you enslave yourself?
Storm: What are you doing?
Apocalypse: Making you stronger. My goddess.
Storm: Yes. You were right. The time has passed. There is no room for gods.
He despairs of our violent ways
Apocalypse: It's always the same. And now all this. No more stones. Not more spears. No more slings. No more swords. No more weapons! No more systems! No more! No more superpowers.
And there's the slim possibility that these weapons might be used against him.
Apocalypse: You can fire your arrows from the Tower of Babel. BUT YOU CAN NEVER STRIKE GOD!
his primary aim is to return humanity to a state of bronze-aged barbarism ~> Why couldn't he achieve that with nuclear weapons?
Commented
May 21, 2017 at 21:20
Apocalypse has disdain for tools and weapons.
Apocalypse: They put so much faith in their... tools and their... machines.
More specifically, he views weapons as a way for the weak to wield power:
Apocalypse: Weapons?
Reporter: Never before has man possess so much power. With Soviet Union and the United States being superpowers...
Apocalypse: Superpowers? The weak have taken the Earth. For this, I was betrayed. False gods. Idols. No more. I have returned.
then:
Apocalypse: It's always the same. And now all this. No more stones. Not more spears. No more slings. No more swords. No more weapons! No more systems! No more! No more superpowers.
On the other hand he is very fond of mutant powers:
Apocalypse: I want you... To feel the full reach of your power. You've only have a taste of your true strength. Unlike others who seek to control you. I want to set you free.
and:
Apocalypse: To tell the strongest among you... Those with the greatest power. This earth will be yours.
It would be hypocritical of him to use nuclear weapons (the tools of the "weak") to achieve his goals. His vision is that the strong will rule and the weak will perish, and the way he defines strength only refers to innate abilities (even if he is enhancing them). It is because of these beliefs that he chooses to use Magneto's power rather than nukes to decimate the planet.
