I've actually thought about doing a rewrite myself in an interactive format before so this is an amazing coincidence! I accidentally found this while reading random Obey Me! fan fiction. I enjoy the headcanons, mostly. More traditional fanfiction is a bit hard to enjoy when it's of an interactive medium with a largely undefined protagonist. Anyway, I LOVED your "telling the brothers they're your favorite" scenario especially so I got curious enough to follow the link and see what someone else had done with the idea.
It's lovely. It captures the original tone and characters well, while providing a new depth. Which is of course what you're going for but it still shocked me what a delight it was to play. I did notice a few bugs and grammar errors, but I'll leave those in the comments.