I feel the same way about the delinquent, I'm not a fan of the effect placed on her being irreversible. Also I don't think the idiot plot point where she gets taken away should happen, especially if the player chooses to forgive her (though I fully understand that keeping the delinquent would be a nightmare for development). Plus that whole sequence is honestly kind of horrifying to me, and pulled me out of the illusion of fantasy. I would maybe implement some other kind of forced separation, or have it be like, a temporary hypnosis caused by a prototype of the device that hasn't fully realized the irreversible nature of the effect to get that boss fight going.
Plus, I think Jane and the delinquent getting together and exploring their discoveries about themselves from that boss fight would be cute, though that alone isn't a good enough reason to justify the headache of changing the game.
So far, I've only stated my personal preference, but I do have one real criticism. The dev notes activated at the end of the game state that the dev felt bad about having the delinquent being a throwaway character in the intro, and kind of just, made her a throwaway character a second time? She shows up in the lab for like, 4 or 5 rooms, and gets sexually assaulted by a robot, abducted by said robot, and then has her character killed by getting permanently mind-altered to the point of not really having much of herself in there anymore, which I find to be a pretty horrifying sequence of events (though, seeing some of the responses here, I might be in the minority on that part).