I've been mulling this over a lot, actually, because I think this is a reason I can't get on board with the ending.
It's like the writers got confused between the difference between omniscience and predetermination.
God in s1 and 2 is omniscient. This means She is all-knowing. She knows what choices we will make, She knows how they will alter events, and She knows how to use that information to turn things to Her advantage. But ultimately, humans have free will, and the choices they make are their own. Knowing something will happen is not the same as making it happen.
We see evidence of this in s1 and 2. The story of Job is a great example. She tests him, She takes everything from him and hurts him, just to see what he will do. She makes a bet with Satan because She knows exactly how it will turn out, but She isn't the one making the choice to stay faithful. Job makes that choice himself.
Predetermination is different from Omniscience. It means that all events and outcomes have already been decided.
In s1 Adam has the choice to put the world back together as it was or blow it up and start over, remaking the world to his ideal.
We see God playing three card monte with the babies. She's stacking the deck in Her favour (assuming that She didn't want the world to end right then) by sequestering Adam away from ethereal and occultish interference. She whispers into Agnes's ear so that a book of prophecy can help supporting characters have the opportunity to arrive just when Adam needs them. But ultimately, the decision is Adam's.
The choice is meaningless if it was predetermined.
Even dog shows he has free will. He is a hellhound; his purpose is to support Adam as he rises to power. But when Adam starts to behave a bit too antichristy, he nopes out.
Adam: Give me back my dog!
Pepper: He's his own dog.
All this to say that S3 completely changed the rules of the world to make the ending fit. They depict God as an unhinged person playing with dolls. That She wrote the book and the outcome is predetermined.
One of Crowley's fundamental beliefs is that the universe deserves to exist. That a 6000 year life span is not enough. He believes it strongly enough to rebel against God, to fall, and when the world is threatened again, to act against his own orders and try to stop it.
And yet at the end of s3 we see him step into the Antichrist's shoes. He has the same choice: put the world back as it was, or blow it up and remake it in his own image. He chooses the latter. His reasoning being that humans don't have free will, and yet s1 and 2 both show definitively that they do. It completely reframes everything that comes before. It makes it meaningless.
And on a personal note, it makes me so sad that after all that time protesting against God's desire to end the world prematurely, he's the one who carries out Her divine will.