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 established settings. Regarding Kyubey's line, "Eventually, you all will join us," there is a high possibility that the Incubators were originally human. Consider our human future as Incubators. 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. Thus, we would try to survive. If the heat death in the setting is considered an increase in entropy, everything with complex functions would be eliminated. If we separate defense mechanisms from emotions—within the context of the setting—what remains for Incubators who have lost emotion is only knowledge and defense mechanisms. This explains the logic of why Incubators cannot have emotions. Next, why use humanity? As mentioned, there is a high possibility Incubators were originally human. If we assume only humans possess emotions, then the target narrows down to humans. Also, to prevent useless entropy increase and maximize efficiency, they utilize "girls," just as depicted in the anime. As for why they gave knowledge to ancient humans, it's the same as Incubators giving knowledge to past Incubators; from there to humans, those humans become Incubators, and the cycle continues to the next humans. Sharp observers might notice—though I can't fully explain it—the point that Incubators might have built time-travel devices. This is purely my interpretation, but if they have technology to utilize emotional energy, they might be able to create tech to return to the past. This is where realistic talk and anime settings diverge. While emotional energy and time travel aren't developed in modern society or even the anime's human world, it's possible a future at the Incubator level could create them. I don't have enough info to explain it further, so I'll stop there. Continuing the thought, the knowledge they cultivated becomes meaningless in the worlds of Madoka and Homura, who rewrote the universe. That is why the Incubators are confused. It's only natural. I've written what I wanted to say, keeping the anime settings in mind. I look forward to your counterarguments!