One interesting plot twist could be that Ginny and Draco's pregnancy is a result of a magical accident. Maybe a spell gone wrong during a battle or an experiment that binds their magical essences together. Another could be that they keep the pregnancy a secret from everyone at first, and as they struggle to come to terms with it, they start to develop unexpected feelings for each other. For example, Draco, who has always been a bit of a snob, realizes Ginny's true strength and kindness through this situation. And Ginny sees a more vulnerable side of Draco that she didn't expect.
A great plot twist might be that the pregnancy is part of a prophecy. It could be that their unborn child is fated to bring about a great change in the wizarding world, either for good or bad. This would put them in a difficult position as they try to protect their child from those who would use or harm it. Also, there could be a plot twist where Ginny and Draco are forced to work together to protect the pregnancy from dark forces. They have to put aside their house differences and past rivalries, which is a huge change for both of them.
Perhaps a plot twist could be that the baby has some unique magical abilities that are not seen in either the Weasley or Malfoy bloodlines. This causes a stir in the wizarding community, with some seeing it as a sign of a new era, while others fear it. Ginny and Draco then have to deal with the added pressure of protecting their child from those who would seek to study or harm it because of these strange powers. They also have to figure out how to raise a child with such extraordinary abilities in a world that may not be ready for it.