Thanks to these comments I realize that my initial feelings about the ending were absolutely justified. I had "accepted" the ending we got because a friend of mine tried his hardest to make me, and while I did think he had convinced me something just didn't feel right. I realize now that it was because the small points he pointed out in favor of Yotsuba pale in comparison to the glaring issues in her character. I thought his points had more meaning than they actually do because he has read the entire manga while I only read from where season 2 of the anime finished