Fridge Logic: Prepare for a huge amount if you don't pause to think about everything while you're watching. The manga is a lot better but still has some plot holes.
For a specific example and one that's kind of called out in-universe, why does the president want to terraform Kimaera? Terraforming is stated to be a big part of the reason that the human lifespan has gone down so far.
He doesn't want to terraform the planet, he wants to alter its specs so it can evolve to be more friendly for humans to survive. What he doesn't know is that the new Chimarean species is doing just fine already without any special DNA. Of course it's not a scientifically very sound plan...
How did Zagi know not to trust Third? Did he know something about his origins? Did they have some kind of interaction in the past? What does Zagi know?