I would make Amygdala more of a direct challenge to Batman's ethos by making him not only a victim of brain damage but also ramp up his strength further with the backstory of him being Gotham's premier power lifter who was mixed up in the underworld betting rings. Have him gain brain damage not through surgery but a powerlift gone wrong which has left him with a learning disability and emotional instability that is controlled for a time before the underworld starts to groom him for crime as he has no where else to go. Batman has to face a mountain of muscle stuck within the predatory grasp of crime families while also being forced to be considerate of how much of victim of circumstance Amygdala is. Have Batman try to find ways to minimize harming Amygdala while preventing him from harming other people to show his more rehabilitative side of his character. Then whenever he is safely subdued it is shown Arkham does not have the staff or resources to properly take care of Amydala and instead release him into "asissted living" which is compromised by the same criminals who used him to begin with. Maybe have an arc where Batman slowly creates a case against Arkham for this short sightedness but then realizes if he did hold them to account it will set a precedent for legal claims from other patients that could cause further loss in resources. Will he open this door to Arkhams destruction for the well being of one victim of exploitation or accept that a damaged system is better than no system at all?