I feel creative tonight, so here’s a back-of-the-envelope Kipo and the Age of Wonderbeasts rewrite:
Let’s start at the top and work our way downwards. What is this story about? The canon doesn’t seem to have an answer beyond “segregation bad, friendship good”.
My answer for a central theme is grief and loss. Let’s actually use the post-apocalyptic setting for something instead of it just being background aesthetic. The story is an allegory for the cultural tension we are currently experiencing, with the world ruined by the older generation who view the strange new young things with fear and repulsion. The humans must accept what they’ve lost and embrace the new mute society instead of pursuing their futile attempts to regain their world by destroying the mutes’. We will parallel this broad-scope theme to personal losses in Kipo’s own story.
So, the first arc is denial. At the macro level, this only requires one change: Kipo’s dad died in the initial attack. Wolf’s oft-stated warnings are correct, and Kipo’s hope that he somehow survived against all odds is naive. Upon this discovery, Kipo swears vengeance on Scarlemagne and pursues him, which is already pretty similar to the canon ending of S1.
We fill this arc by expanding Kipo’s interactions with the mute societies, and using the episodic encounters to actually make the worldbuilding make sense. The theme of denial is integrated through Kipo’s continued attempts to resolve conflicts peacefully despite all advice to the contrary. Crucially, nonviolence does not work perfectly. Perhaps it does lead to the mutes allowing her safe passage, but they are not best friends forever and she does not change their opinion of humans; the next humans who pass through are still gonna get eaten. Kipo is applying a band-aid to the situation, not providing any permanent solution. This can be revisited in future arcs to show the consequences of her denial.
Second arc, anger. Kipo joins the human resistance early on and fully embraces their mission to defeat Scarlemagne. Without Lio to explain things, the journal can actually be a meaningfully-timed reveal about the full nature of her powers in addition to the reveal about her mom (if we’re keeping that). The need for the anchor also becomes more relevant if her dad is completely gone and this is her only tangible reminder of him.
Kipo leads the charge to Scarlemagne and clashes with him. Circumstances require her to go full jaguar to defeat him, at which point she readies to kill him. Her friends go through the whole cliche of trying to talk her down, “This isn’t you!” “If you kill him you’ll be just like him!” “You can’t fight hate with hate!” etc. Kipo kills Scarlemagne anyway, losing herself to the mega jaguar and running off. (To make this more palatable, we could change Scarlemagne’s backstory to be less sympathetic, perhaps removing his connection to Lio entirely. Or we could keep his backstory as-is and embrace the moral grayness!)
Third arc, bargaining. Kipo and her friends must find a way to bring Kipo back, and in the process Kipo must make sacrifices and face hard questions about who she really is and what she has to leave behind. This is paralleled with the reveal of Emilia’s treachery -- for pacing, she probably shouldn’t be revealed as explicitly evil until now. Emilia and her human resistance are desperately clutching for the world they destroyed, trying to bring it back no matter the cost.
She, Kipo, and the other humans must ultimately come to accept that some things can’t be taken back. They destroyed the world and they have to come to terms with that sin. But in their blind nostalgia, they couldn’t see that life has gone on and a perfectly fine society already exists: the mutes’. (This would, of course, require mute society to be actually functional and for industry and innovation to exist outside of Scarlemagne, which we can establish in earlier seasons.) Kipo, as the bridge between their worlds, is able to fully integrate human and mute society, allowing everyone to live prosperously once more. For bonus transhumanism, mutating humanity into a new form like Kipo may be required, similarly to how Adventure Time handled a similar plot point.
Also, Benson doesn’t exist because he’s a completely extraneous character and literally everything he does can be handled by Wolf or Dave. His important moments are actually stronger coming from them, honestly -- a mute inviting Kipo to the theme park to show her the surface has good parts carries a lot more weight than a human doing it. If you still want gayness, Kipo/Wolf is endgame.
(Additionally, as much as I love representation, maybe let’s not have a black girl’s character arc be #NotAllMutes. We can conserve representation by having Kipo actually look Black/Asian instead of a white girl dipped in grape juice.)
So there you have it. A thematically coherent story with topical social commentary and several dark subversions to keep seasoned audiences’ interest.