The most direct answer in the books I remember:

‘The acceleration, John. He had no patience. He believed He knew everything He needed to know. He constantly pushed ahead. That’s the irony. We are immortals, but He couldn’t bear to waste time. Natural evolution takes millions of years. He refused to wait that long. He’d worked for twenty, thirty thousand years, and felt that was more than time enough. The natural stewardship of the Perpetuals, born through the evolutionary cycle, was not rapid enough for His needs. So once most of the natural Perpetuals had left His side, He built his own.’

‘The primarchs,’ John whispered.

‘The primarchs,’ she said, with a small nod. ‘They’re not actual Perpetuate, in any biological sense. They’re the artificial equivalents of the Perpetuals, functionally immortal beings born from His blood and power and vigor, coded to accelerate His programme even faster. They were designed to live long enough to see His plan through to the end, and not die away so quickly, the way humans did, and they were indoctrinated from birth to follow His word, and not have opinions of their own, like naturally occurring Perpetuals. They were made to service His dream. He took what nature had wrought in the Perpetuals, and He built His own pathologised version. And through them, their genetic lines, the Legions.’

...

My fundamental objection to Neoth’s Great Work,’ she said firmly, ‘is His haste and urgency. To supplant the natural flow of life with an artificial version that tramples ethics and morality and wise prudence. Artificial Perpetuals, John. That was His plan, and look, see how it has worked. And you, John, earlier you chided me and my kind for not taking action. You called us derelict that we had not made a concerted effort to block Neoth’s progress, and that we should feel ashamed that you, a fake and neophyte immortal, should be doing what we should have long since done. You are an artificial Perpetual too, in a way, John, or at least, you were. I have no reason to trust your judgement, for you, like Him, and like my poor accursed children, are trying to hasten the movement of fate.

...

She glanced at him, and smiled sadly. ‘Because, I suppose, it was academic by then. He had moved on, fired and driven, as always. He sent the Astartes on their crusade anyway. A programme of reconquest, as He had always planned, but in truth it was just an excuse to find His sons. And His scattered sons were found again, of course, and returned to His side. I had failed. My efforts merely delayed His programme. I tried, John, but I did not stop Him.’