As mentioned in the first world A chapter, emotions is something new for machines. In this chapter it's mentioned that they only learned how to cook recently because for them stuff like taste didn't matter, they only cared about "living" efficiently: keeping their body functional and healthy, working, marrying and having kids, all that not out of desires but because it's their task to be the human in the human's place, thus they are soulless. It's not necessarily the spiritual-religious sense of the human soul, but in the artificiality and pointlessness of those lives.
Since it's implied that the A.I. are learning emotions (and humans continue to disappear in fake dream worlds), they are going to become the new dominant species with their own "souls" that either perfectly mimics humanity or that is something unique, and therefore things will eventually end up fine (but not for the real humans). And Yukiko by actually learning directly from human beings (and maybe having the most advanced tech as well) was able to evolve faster than the rest in actually developing her own free will (more than the ability to just make -pointless - decisions that all A.I. already had).