Option to not pistol whip Gavin Archer after letting him keep David. Just because I'm okay with letting him experiment on his autistic brother doesn't mean I'm okay with pointless brutality. I would have appreciated it being an interrupt instead, like what Paragon's get.
Option to reprimand Jack/Garrus for causing trouble with Miranda at the start of the Suicide Mission. It would have been fine if they had said that it's Shepard's decision or that someone else is more qualified, but they just act like brats. Alternatively, let me send them through the vents.
Option to send Joker to therapy for being a pervert/robophile and not let him come back until he has dealt with his "urges".
Option to call out Cortez for being an attention seeker by playing his husband's last message in public. I'm sure headphones still exist in the future and I'm sure he would have heard Shepard coming... the lift is right next to him.
Option to not call in the Normandy if EDI is damaged during the beam run.
Option to get revenge on Jack after Grissom Academy for punching and humiliating Shepard in front of her students.