About the villain's endgame. It in fact doesn't have logic and is doomed to fail because it's based on a childish reasoning. And just like with Svetta's world, if you have a strong enough will you can overcome it (author is probably into Evangelion and shit). The children themselves would probably be able to free themselves once they realise the truth, probably inspired by the heroes.
I'm not sure if the author is doing it on purpose and wants to write the narrative around this, but she just made her final villain into the real underdog of this manga. He is dangerous and can cause harm to the heroes but his own endgame is doomed to fail.
Now my main complaint is how shallow and black and white Stigma's goal is being presented. Right now there's no nuance to the "I want to create an utopia and you're in the way" and as we've seen in this arc, no sad backstory will be enough to solve this. The heroes are and will be right against Stigma as they were against Svetta. I hope the author can prove me wrong and insert a good twist along the way, or just turn Stigma into a set up for a true final boss.