I will write down my thoughts regarding Kyubey. First, as a premise, I prioritize the settings within the anime, so there may be parts that differ from realistic logic, but please understand that these are the settings. Kyubey's line, "Eventually, you all will join us," suggests a high possibility that Incubators were originally human. First, consider if the future of us humans is the Incubator. We have defense mechanisms to protect our species. Protecting ourselves is natural, and the death of the universe would mean our extinction, which the defense mechanism flags as a danger. Therefore, we would try to survive somehow. If the heat death in the setting is considered an increase in entropy, everything with complex functions would be eliminated. Let's separate defense mechanisms and emotions for a moment—this is within the setting. For Incubators who have lost their emotions, only knowledge and defense mechanisms remain. This makes the logic that Incubators cannot have emotions predictable. Next, why do they use humanity? As written before, it's because there's a high possibility Incubators were originally human. In other words, if we assume only humans possess emotions, then the targets are narrowed down to humans. Also, to prevent useless entropy increase and gain efficiency, they use "girls." This is as depicted in the anime. And the question of why they gave knowledge to ancient humans—it's the same as Incubators giving knowledge to past Incubators, which goes to humans, who then become Incubators, and the cycle continues to the next humans. Sharp observers might notice, though I can't fully explain it, that Incubators might have been able to create time travel devices. This is purely my interpretation, but if they have the technology to utilize emotional energy, they might be able to create technology to return to the past. This is where realistic talk and anime setting talk diverge. Technology to use emotional energy and technology to go to the past are not yet developed in modern society, nor in the world of the anime, but in an Incubator-level future, there is a slight possibility they could be created. I don't have enough information to explain this further, so I'll end it here. Continuing the story, for that reason, the knowledge they cultivated becomes meaningless in the world of Madoka and Homura, who rewrote the world. That's why the Incubators are bewildered. Naturally. I've written what I wanted to say, but this is strictly considering the settings within the anime. I look forward to your counter-arguments!