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My goodness, I didn't expect you to reply so fast and so thoroughly too! I'm glad if my feedback can be useful and/or can make you feel good!

I actually wanted to edit my comment, because I've explored Roya's other endings in the meanwhile. The normal ending really had an impact on me, it showed that despite his doubling down at first, as time passed, the need for revenge is no more and there's only regret and loneliness ;; I realized how much of a sweetheart and just a lost boy Roya is at his core, and how fate had been unfair to him to send him down such an awful path. Makes me wanna wrap him in a blanket and cuddle him. So he really, really needs and deserves that time travel redo and nudging in the right direction ;; 

Speaking of the programming tweaks, playing the random game with Roya by the pool was a fun part! 
I don't remember many details from the original game, but I'm definitely going to replay it soon! For nostalgia's sake, and because of Junoru, I recalled some details from his route, since obviously he shares his backstory with Roya, and also recalled how much of a sweet gentleman he is and I kinda miss him. I don't even fully remember Roya's fate there... I'll deal with that emotionally once I get there in my replay. (I realize it may be worse going back too, RIP my heart.)

There's really lots of love and care and time and resources you're putting in this game to make it as gorgeous as it is!
Oh, now I'll be even more curious about those extra stories!
I think it's okay for characters to make mistakes and wrong turns before finding the right path, as long as the choice they make makes sense for them. It really depends on the type of story you want to tell. Your MC is quite the logical and straightforward person too, so a straightforward solution works well here! Misunderstandings are just so frustrating, I agree, they feel like an artificial way to create conflict. Btw, I don't think you need to worry too much about your writing, I see many people fanpersoning in your comments, you've created a much beloved world and characters and story! (Sorry if I came off as nitpicking, I just used to dabble in writing so that's what I focus on most. Also I take back the "forgiving the ace twins too easily", found the branch where it's talked out in detail. I only ever wrote linear stories, mostly fanfic, I imagine it's much harder to keep in mind what events and conversations happened on every single branch...)

Haha, Chain seems to take cold hard logic and efficiency to the extreme, from what I saw here and remember from the original game (I don't even know whose route it was, but I remember MC convincing him to come help, and he eventually did, without much of an explanation). It makes me really curious how he'll behave in a romance situation. And I imagine the story will be quite different from the police/"hunter"/non-supernatural perspetive. But that's for another day. I might come ramble about his route later!