Sure, Chrysalis was a mean, vindictive, tyrannical bitch who ruled over her minions with an iron hoof and planned much, much worse for the ponies that stood in her way of total domination. However, since she'd come to look to you for love, to see what someone giving love of their own free will was like, she was changing. Yes, obviously she had changed physically, but internally she'd begun to show affection for others, primarily you... almost exclusively you, but her children, which she had already loved in the path, she now showed more devotion. You knew this all too well, because... well, she was you.