"parents suck, kids should stick together and look out for each other instead"

aka

puberty, as solbowz said.

EDIT: That's being a bit unfair, since Himari's status as the frail macguffin tempered with the Princess of the Crystal personality is more interesting, as well as the capitalist-medical system that the good Doctor builds around her. That's the better part of the show, as well as how Himari tends to drift into a liminal space (that scene in the library is the best in the show),and be equated with a goddess of sorts (though Momoka and her significance is never really explained -- I'm willing to overlook that in the name of magic realism and just accept it).
Even Himari is kind of hamstrung a lit bit by the forced revelation of "oh, I don't actually care about Kanba, I really love Shouma" that comes out of literally nowhere and has almost no relevance to anything. >_>

The show has some good ideas and some characters that could be been really compelling (Why not explore Mario and Momoka's "other side" more? Why have the extreme fake and superficial motivations/characters that don't really do anything other than act as vessels for the extremely stupid/simple message pointed out above (the grandfather, Yuri, teacher dude).
Penguinforce/the bad guys in general is a really wasted plotline with no more motivation other than Sanetoshi ranting about how people live in boxes and therefore you have to kill them to break them out of their boxes. It would've been much more relevant and neatly constructed if they made them an environmental extremist group bent on wiping out humanity except for their group (lol Rainbow Six), considering they were an Antarctic expedition group (discovery and initial resolution), the significance of penguins (to tie into that), and the violence. You could even parallel the abuse of parents to children as the way humans take care of the planet, and thus explain Sanetoshi's interest in abandoned children as a kind of extension to a poisoned planet he's trying to save (in this scenario).

Though this anime was jRPG and cliche as hell, it was still satisfying. It even managed to properly handle its themes, as simple as they were, of people going through a love of battle but ultimately realizing that other things were more important. Not to mention it was visually very cool and the soundtrack is one of the best I've heard in a while.
Red Chaika snapping black Chaika's neck with a kick. Gaz linking up all the satellites. Gaz's magic against Toru. Even Niva -- as close to a literal tool as you can get, asserting her agency and personality and siding with Chaika. Cheesy, but man was it graphically sick. Also, Frederica getting chopped in three but dragging herself around to try to protect Toru.
I kind of wish Chaika had just straight-up died, sacrificing herself. That would've been an extremely poignant and bittersweet ending, but I guess her losing all her memories is still pretty good.
Red Chaika is so tsuntsun but cute. Looks like she found employment with that hero's vineyard (really subtle way of telling us that, too).
Akari is the hero we deserve, I lost it at "This is just the prologue."

The only thing I can really complain about when it comes to watching Kino's Journey is the lingering shots of text.

Well, there's also the fact that this show wants me to hate society. That can get a bit weird.