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!