I don't... really think there's anything mysterious about this manga's plot, at all? A guy's older stepsister is a troubled teenager, he works to help her and bring her back into the family, what is anything other than crystal clear about this?
Next you'll ask how the hell the prof can see this now, but was unable to see that throughout the guy's tenure at the academy.
Look booba! Schoolgirl oppai! Pew-pew! Story? What story?
None of her behaviour in their little relationship, from guilt-tripping the MC for not guessing the emotional needs she had refused to communicate to staying the night with another man without as much as a call, paint her as a nice person. There's being inexperienced, and then there's being...