You know I disagree, since some of the problems are with the basic background of the characters it will take more as a few tweaks and story changes to start making sense and to bring some characters back into territory where you can turn them around with good writing from hated chars into chars you can love and want a relation with which is the goal of a harem after all within the story. Let alone bring back Alice to a char you want to save instead of let her stew in her own juices, as a player which goes against the goals of game.
It also needs remake of MC into someone you can relate to as just feel pity for and it is believable he will grow up some instead of from having to go from an 8 yo mentally into an adult even with help of a mentor with all the implications that him being an 8yo mentally at 20 yo has on all those milfs (yeah to an extent it hits all that so called cared for him) around him that so called loved him but were powerless or unknowing to help him last 10 years.
Saving those characters around him that so called cared for him also means you will have to redo major part Sofia storyline and so on. It is not just a tweak, making an excuse or such, unless you want a dark revenge harem where MC exploits guilt, negativity and punishes people for fact they were at best uncaring or even evil in reality to him whatever they say, cry or hug him to death instead of a loving harem game.