Yeah, there's a lot of clipping in Illusion games, like Honey Select, and it makes the animation become terrible, so i see your point. I just wish they could make all the characters share animations, at least, or have the same amount. I mean, Anya is my favorite, and she has so few animations, unlike Alet, who has a ton of them.The issue with body customization is that clipping may occur easily with certain animations. For instance where the partner in a sex animation is grabbing the breasts, if you set the breasts too large the fingers will go right into them, and when they're too small the hands won't touch. I don't think there's absolutely no solution to this problem at all, but I haven't seen it done well enough yet.
Another reason why they may not do that is to keep the characters separate from each other. Have each of them have their own appearance, you know. By giving the ability to change their appearance, you sort of take away some of their individuality. Don't know if I explained that right. But there's a reason they have these characters and they have their own backstory and such.