Playing as a female, if you're mostly light, Mira notices your light side glow and asks if you were "intimate" with Atton. You can tell her that you don't have that kind of relationship because Atton's like a brother. Like an idiot brother. (That's why we love Atton.)
On Dantooine, when the Disciple offered to join me, Atton yelled that he was so excited that the Disciple was coming with us, he was going to throw a big celebration. I wish I could trigger a cutscene where Atton and the Disciple actually talk to each other -- I don't think the Disciple is equipped to deal with sarcasm.
