I never understood the whole Queen/Ripley reproductive process. In Alien: Resurrection, the newborn brutally kills the Queen after she gives birth to it. Surprisingly, it has human characteristics. Why does it acknowledge Ripley as its mum if the Queen gave birth to it?
The novelisation strongly indicates that it's because the newborn feels a greater psychic connection to Ripley than the Alien Queen. It recognised Ripley as the Queen and the Alien Queen simply as a threat and potential food source:
That was when the telepathic connection slithered through, touching her [Ripley's] mind, whispering to her of genetic bonds she could not deny. And then it was all right there. Her longing for the steaming warmth of the crèche, the strength and safety of her own kind. Just a moment before she had suffered the aloneness of her own individuality. But now she was given the chance, again, too in them, rejoice with them. She was in the crèche. She could reunite with the warriors, and serve as the Queen, nurturer of the Newborn. That was why she had lived. Because this shell that was human, this Ripley, was the mother of them all. The first womb. The first warrior. And she had lived long enough to know it all, to share the glory with them. Ripley was the keystone of the hive. The nurturer of the crèche. The foundation of the Newborn.This was the answer to the question she'd been asking. Why? This was why.
She gazed into the liquid brown eyes that could have been her own, and reached out a hand, placing it on the Newborn's skull. Her hand slid over the long, Alien head, patting it as she once had done to Amy's, stroking it as she once had done to Newt. This was her child, just as they were.The Newborn uttered a soft mewling sound, and gazed at her, and Ripley felt the telepathic connection deepen, grow stronger. It was so different from the others, yet the same. But there was something more in this contact, something undeniably human.
It was like being connected to a part of herself, a warped, malevolent part that was bonded to all her fierce self-preservation, all her intense determination.