Antimony's refusal to accept help from the adult staff at the Court, and why she went about trying to solve mysteries all by her lonesome can be confusing at first. It's often dismissed as simply necessary to keep the entire story from being resolved in two chapters. Then, about the time that Ch 14 was going up, it becomes clear that Annie's independent nature was a result of her unusual childhood—her years at Good Hope Hospital had taught her to solve her own (and other people's) problems all by herself. But what's really brilliant is the realization that because she doesn't seek help from the adults who actually know what's going on, Annie's solo snooping and problem-solving actually makes things worse: She nearly gets killed a few times, and then she almost triggers a diplomatic incident between the Court and the Woods. In other words, the "kids are smart and Adults Are Useless" setup was actually being deconstructed by the comic. It also helps that in later chapters, Annie seems to be maturing and learning to accept help and advice from other.
From scenes in the ether, it's apparent that a person's appearance in the ether is in some way connected to their nature or character. In particular, their hair: Annie's hair seems to be infinitely long, while Anja's and Parley's hair in the ether is longer than their physical hair, but not infinitely so. Also, the separation between the physical world and the ether is weaker in Gillitie Wood, particularly for creatures of the etherium, like Suicide Fairies. In light of that, the freakout over Red's hair in Ch 15 ("Your hair! It goes up again!") takes on a completely different meaning: Blue wasn't pushing Red away (solely) because she's shallow. Blue was pushing Red away because she came from a world where personal appearance is inextricably linked to character and personality, and she failed to realize that this was not true in the human world.
Shadow 2 was vital for creating the story of the webcomic itself. See, if Annie was not inclined to confront him that night in the hallway, we would have never figured out that he needed to get across the bridge. And if we never figured that out, Annie would have never built a robot for him to ride across. If Robot had never gone across the bridge in the first place, he wouldn't have come back across in chapter seven. Annie would have never fallen off the bridge, making it so Coyote and Ysengrin never organized a meeting, and Coyote would have not invited her to the forest to expand her knowledge of her etheric powers. Along with that, Annie would have not discovered Jeanne, or have a reason to create a new body for Robot, and Kat and Annie would have never located Jeanne's shrine or learned about the story of Diego.
When Robot and the others see Kat taking care of Jeanne's shrine, they interpret her as an angel. Because she's beautiful, sure, but in religious texts, there are three ranks of angels that serve to guard and protect God. To them, Diego is a father, but Jeanne is a friggin deity. And if Diego built them to love her just as he does...well...
The robots said that "the court grew from the seed Bismuth." Bismuth is a metal that chemically resembles antimony.
In "Give and Take" the resurrected robot describes the robots we've seen in the series as "elegant designs", as well as other superlative adjectives. This seems almost funny at first to the reader, as the resurrected robot (who belongs to the robots created by Diego himself) looks impressive and majestic while the modern robots look like cubes at worst and pragmatic at best, in the case of S-13. The thing is, the robot has different criteria than the human one. For him a good design is one that works best in its own movement and its functions, and the modern ones are probably this. He looks better on a human aesthetic, which would be superfluous on the eyes of a robot. So, indeed, modern robots have a more wonderful design.
Consider the storyline of Chapter 13: Kat meets a boy, develops affection for him (whether it be a crush or "real" love, it still affects her quite a bit), but eventually has to let him go due to circumstances beyond her control. In comparison, consider Diego's story: he meets Jeanne, develops affection for her, but eventually realizes that she will never return the affection. And finally, think of the difference between their reactions: Kat accepts the loss with surprising equilibrium whereas Diego basically ruins everything for Jeanne as well as for himself. It seems that Chapter 13 is a way of comparing/contrasting Kat's personality with Diego's, especially given how both of them are heavily involved with the robots.
Why do Jones's x-rays look like this? It's not because she's completely solid, made of some uniform material: it's because the x-rays, like everything else, can't penetrate her skin.
Of course Reynardine supports same-sex relationships. He's a fox who fell in love with a human woman. He's the last person that should criticize an unusual union.
Mort feels satisfied with his time on Earth now because this is about when he would have died of old age.
Mort's first appearance occurs in a hallway with three words in Latin ("Dulce et decorum") written on the wall. Those are the first words of a famous poem, written in the wake of WWI, about the evil of war. At the time, it seems like an odd but creepy touch. In retrospect, it's suggestive of just how far in advance the comic was planned.
Reynardine stated that everyone knew that having Antimony would kill Surma. Including, in his words, "[Annie's] damned father! Especially him!" Especially? Does this mean he always knew having a kid with Surma would kill her, and simply didn't care? There's also the implication that as of a man of science, he thought he could defeat the process, allowing Surma to live with Annie normally. He failed, which would be part of the reason he abandoned his daughter (she's a very strong reminder of that failure, not to mention his dead wife). His guilt is somewhat ameliorated by the fact that "everyone" includes Surma. Whether the fact that it was just a risk that both of them were willing to take makes the fridge horror better or worse is debatable.
It's funny that they chose to name her Antimony, which is a highly toxic chemical element. Could have a nasty undertone when you realise Annie's existence caused her mother's death. Surma's own name is kind of unfortunate, as well. In Finnish it means "unnatural death".
Coyote's Establishing Character Moment in The Fangs of Summertime is when he bursts out laughing after hearing that Antimony is Surma's daughter, cracking a joke about Mr. Eglamore being her father. Once you get to The Reveal, however, this makes that scene much more disturbing, as it means Coyote just learned that Surma was either dead or dying, and he doesn't care at ALL. Even without the scene mentioned above where he removes Ysengrin's memory, it's still quite obvious that Coyote is much more evil than he initially appears to be.
With the revelation that spirits brought to the ether forget about their lives, several of Annie's references to missing her mother in earlier chapters take on another light: Because Annie had to personally bring her mother to the ether, she would have had to watch as Surma forgot about everything she'd shared with Annie, including the fact that the girl was her daughter.