When the player picks dialogue options that tend to up the Fate Link with one of the characters, the protagonist's sprite always smiles and looks sideways. Seems strange that he isn't smiling at them, then one realizes that he's looking at the player to say 'Good choice'.
The first time the player can encounter Joe, before being officially introduced to him, one of the options to his dialogue is 'Long time, no see'. This option increases your relationship with him, but it overall makes no sense to say this to a stranger. Then you realize with New Game Plus, especially with the Restorer ending, that the protagonist and rest of the characters are likely still holding the memories of the previous 'cycle' and really did meet before.
Miyako's design was done by the same artists as the other characters, but her lines are thicker and she oddly stands out to the rest. Could be a case of the art-style altering slightly, but it could make sense. She's basically a glitch in the universe's compter; Cor Caroli mixed into a human appearance to fill in a role. She's not supposed to exist to begin with, obviously she'd look weird compared to others.
Joe siding with Ronaldo:
Why does Joe sympathize with Ronaldo? Joe is a guy who, by most metrics of society, is very successful; He attended a prestigious university and gotten an important and high-paying job. And as he himself states, all of that was purely due to dumb luck and not any kind of talent or hard work on his part. He's basically Timothy Dexter if he were actually self-aware. It makes sense for him to be skeptical of Yamato's view of the world as "strong" people versus "parasites"; he's living proof that getting ahead may not reflect anything about you.
Another important reason is because Joe's girlfriend. By all accounts, Joe's girlfriend, being a sickly person who needs help to survive would be labeled a "parasite" under Yamato's views, and although Joe is insecure about his girlfriend to a degree, he very clearly loves her. In Ronaldo's society, she has better chances of living and being able to maybe improve, while Yamato's merit focused system would leave her behind to die for being "weak". Naturally, he picks one of the two that would give her better odds of being happier.
Polaris is easier to fight on the Restorer, Meritocratic and Egalitarian endings, because you're playing along with her trials to prove your worth to reshape the world. This can also explain why she survives after her defeat, since it's all a test for humanity. The fight's a lot harder on the Kingmaker and Liberator endings because Polaris's life is at stake and there's no reason for her to hold back.
It's obvious and happening as one proceeds through the game, but just the idea that the world is being swallowed up into the void practically the entire time can take a while to really hit the player. Just think, it's going on while the characters are sleeping or socializing.
The Liberator ending. Well, the world is not being swallowed up into the void anymore. But Polaris is dead. The only thing remaining is a rather small piece of land and the rest of the world is now nothing but a large ocean, full of water that is most likely undrinkable. And there is no Polaris, Septentriones or any supernatural thing here anymore to save anyone. Meaning, the world cannot restore itself, it will remain like this. My God, What Have We Done!?
In the Triangulum Arc, Miyako goes through some when Yamato returns from the Akashic Stratum. Since she's a Yamato-Replacement, she goes through the idea that her own existence will suddenly glitch out, due to the paradox of there technically being 'two' Yamatos now. Just trying to wonder what she might be going through is horrifying.
In the Triangulum Arc, it's even treated in-universe as one: the revelation that the world they are in has been regressed twice. That the Triangulum attacked after the first regression, that the protagonist didn't exist in that world and that everyone except for Yamato and the Anguished One died during that cycle. The characters do not take well to that news themselves.
