Hi friend, thank you for leaving a comment on my little fic! Anytime I receive anything from anyone always makes my day, so I'm grateful you took the time out of your day to write all of this in response to the piece. I was going to leave what I said here as a reply to what you put in AO3, but I thought I may as well put it here since I am a Nagisa Shingetsu blog after all, eheh.
I really enjoy writing and just wondering 'bout Nagisa and Kotoko's relationship as well, they bounce off each other extremely well (and not to mention their directly contrasting color palette always makes art of them very pleasing to look at) and I think they're probably the relationship between the Warriors of Hope I enjoy dissecting the most apart from Nagisa and Monaca; but that one has a completely different set of reasons in comparison to why I like to look at how Nagisa and Kotoko play off of each other.
One thing that you brought up that I'm glad you managed to catch (I wasn't sure if I even wrote it well enough, to be honest, so this is reassuring) is how Kotoko's need to put up a front in front of everyone stops any of Nagisa's attempts at trying to ask her why she seems so offput, and she knows Nagisa well enough to say something that'll distract him from pushing the subject even further, because at this stage of UDG, she doesn't really feel like opening up to him just yet; and she knows it's not a fault of Nagisa's by any means, it's just something she really struggles to do. "I won't do anything you don't want me to do" is one of the few pieces of dialogue I used, because I wanted to put that on a spotlight since I feel that's a promise that Kotoko has heard plenty of times in her life but always gets shattered, so when Nagisa says it; it makes her want to raise that shield to protect herself even more, yanno?
On that note; yes, wholeheartedly agree about how Nagisa and Kotoko having something they can learn from each other. Nagisa has a lot of things he wants to accomplish - paradise, approval of others, and self-fulfillment but he doesn't truly take initiative to do any of that until later on when Kotoko gets beaten + spared by Komaru and Toko, and he decides that enough is enough and makes the call to just allow an exit.
Kotoko on the other hand actively hunted Komaru down (and targeted her for... er, very specific reasons that I won't get into since that whole plotpoint is a mess) and didn't really have any reason to put her faith in any of the other Warriors of Hope (childishly beefed with Masaru, outright dislikes Jataro, thinks Nagisa's boring, and an unhealthy struggle with Monaca) until Nagisa steps in, puts her safety before anything else and tells her to stay out so she doesn't end up getting hurt by Monaca. And for Kotoko to see Nagisa not only defy Monaca's game knowing just how much Nagisa cares about Monaca's opinion of him?
That's a very, very strong case for where that trust between the two of them can seriously start to sprout because Kotoko now knows that Nagisa is willing to risk his own image and his crush's opinion of him not only to protect her, but for the paradise. Heck, I'm kind of diving into headcanon/indulgent territory at this point, but I'd like to think that now she sees just how much Nagisa was willing to fight for his ideals, she now knows she wants to share those ideals of a children's paradise with him as well (she talks very strongly about the paradise in Chapter 5 after Komaru and Toko rescue her - where she reveals Monaca didn't care about the paradise at all. Mind you this is the first time we see her after the scene with Nagisa, and I don't think she's as passionate about the idea of paradise as much as she was with just killing adults until Nagisa stepped in).
That's essentially what completes both of them in the points that you mentioned, Nagisa now has the guts to fight for what he wants to achieve/protect, and by seeing that; not only can Kotoko now feel safer around him, but it now lets her know what she can fight for.
Sorry that got so long; you need not reply to any of this, I just ended up going on a tangent because there's a lot to talk about when it comes to these two and I wanted to express it here since I worry that I don't get to put out all of it when I'm writing. I'm glad to have finally gotten back into the groove of things again though. Thanks again for everything!