For a first attempt at a VN, this is fantastic. Your vision comes across clearly. You integrated subtle changes into the sprites that didn't feel meaningfully out of place, and your stylistic shadow sprites gave an edge to the flashbacks, as though a child's dreams filtered their perceptions of the suffering.
I understand resource-wise why that continued into the present for the bull, but I would have liked an actual head on his shoulders to help accompany Unagi's understanding of his growth, how he was no longer bound by the shackles of his fear at his former captors.
A lot of the elements of the story were designed to shape the encounter with the colossus: what Unagi was leaving behind (his savior cum lover), what he had already left behind (manny and the dragon, still residents of the old new world), and what he wanted (revenge at the unjust world), about shaping where he was in relationship to others. How does this man fly alone? The unsaid rules of the world that binds him in place, that you still have to work with.
I'm surmising this was the attempt of the 'chess narrative', because if it wasn't, that part wasn't working for me. We got it so close to the end that I was expecting a more literal narrative adjustment-- to try and break through the colossus, the rules that were thought to be understood were wrong. The Flying General had to be possible "in real life" to allow for a paradigm shift to defeat the colossus, and yet we were left with a different paradigm, of Unagi reorienting the world around himself while Cody could now only reasonably sit on the back lines from then on, a clash that unsatisfyingly faded into another day's ending. That doesn't make it less realistic, but I feel like it doesn't go towards where the piece is taking me. It's pointing towards a need to escape the boundaries that were set in place, but the results are roughly an altered status quo.
It doesn't fulfill the promise of Unagi's reckless rage that Cody has observed, an impending death as a confirmation of the life deprived of privilege he's stuck with nor the promise of seeking a sufficient paradigm shift, looking for what the world could be (departing being a seeker altogether and going to be a sort of hero for the common men, like Cody to Unagi in his youth) and giving up the untenable position of being a seeker OR the shonen anime ending of grasping victory from the jaws of defeat. Instead, we get what feels like new status quo, same as the old status quo.
The romance is unsettling, to me. Cody saves Unagi at an age where he's still able to be a child sold by his parents -- I'd say early teens at latest. Cody hits his seeker's limit at 28. He's what, seven years older by a reasonable guestimate as he was training from childhood to learn his seeker capacities and it must take a reasonable amount of time for someone with no training to become sufficiently competent to fight against the mecha with him. Unagi expresses his rage at the world (an unjustness of the society they were born into) and Cody's response is "I love you". Like, I'm not sure if the whole work was meant to portray Cody as socially incompetent because with each thing he says, he comes off worse to me. The mentor/mentee trope can be difficult to navigate, let alone when it comes with a sort of savior complex.
I think your premise is tons of fun, and you did a great job with the materials you had (let alone found and modified) and your collab with Hugh, but I think you failed to fulfill the promises the story setup, especially in the ones setup not long before the end of the piece (the 'chess' scene).
I also don't know if it would have been better or worse if the Seeker's limit ended up a higher age (to move away from the sort of biological realism 28 implied), because that could have aged them up to a point where the relationship felt less uncomfortable, but then you'd have to lean more into the trappings of xianxia that seemed to underlie the fighting capabilities (and the greater genre in itself), whereas I think the tenuous zone the piece has resided in lends strengths that embracing the xianxia genre would not.
Like sorry, I'm not trying to underscore the great work you did here in my reiterations. I think it bears repeating you did a great job here, even if I didn't feel narratively sated, and I think it's obvious why others have bought in the way they did.