I think using Tsukuyomi is Itachi's way of showing respect for a fellow being. Like when Itachi used it on Kakashi. He didn't kill Kakashi but instead just messed him up psychologically. And when he did it on Sasuke, Itachi just wanted to remind Sasuke of how much he loved Sasuke by showing him the past and how he showed so much affection towards him and no one else.